Things Learned from a Gulf of Mexico Science Conference

One

The preliminary results are in on the Deepwater Horizon oil spill.

There basically wasn't any hugely negative impact to wildlife in the immediate aftermath of last summer's oil spill. Some stuff died because the oil was toxic, but other stuff stepped right up because the oil was food. A lot of stuff that looked like it ought to be affected ... wasn't. The stuff that was knocked down recovered within a few months after they capped it. In short, some short-term changes in ecological composition occurred, but no overall increases or decreases of anything.

Also, commercially important fish had an outstanding year due to the lack of commercial fishing.

This is not to say that the Gulf ate the oil and is just fine now. Although there weren't immediate effects, the oil is still there and will likely have longer-term chronic effects. Some fisheries might not collapse until a couple years later, depending on how long the life cycles work for the seafood involved.

Two

The next time I find myself on the job market, all I really have to do is show up to a science conference and talk to people about what I can do with their CTD data. Voila, jobs will magically appear! Send out resumes? Phhht.

Grade School Science Fairs

When I was in 8th grade (age 14), my school held a science fair. My project was about the growth of mold in four different drinks - milk, orange juice, apple juice, and grape juice - in glass bottles that were both capped and uncapped. These resided on a shelf in my bedroom for a month and the smell was terrible, and also I couldn't drink apple juice or grape juice again for a very long time. And I got a D. >.> Being as I was a child of restaurant owners, and being as I was in a college town where half the other kids had university professors for parents, well, my crappy little handwritten poster just didn't look all that good next to, say, the sophisticated microbiology project with the gigantic professional-looking poster with petri plates in front of it. And my grasp of proper scientific format was nonexistent at the time.

All of which came to mind during my second experience with a grade school science fair, which was today. This time, though, I was one of the judges.

The projects were interesting and varied, and about on the same level as my project probably was. They grew plants, grew mold, tested for conductivity in things, tested for differences between different brands of various products (toilet paper was popular for some reason), and also wrote reports about volcanoes. It was fun seeing what their perspective was on things, when they didn't quite have all the knowledge that you'd expect in the average adult. :)

A walk in a park

Despite having lived in Savannah for 8 years, and even though I used to drive past it every day, I'd never visited the Skidaway Island State Park until today. When I got up, though, it was sunny and warm (60s F / 18ish C). It's also right after a week of below-freezing nighttime temperatures, which means many fewer bugs. And I wanted to be outside. So ...


Coastal Georgia is basically all salt marshes - think of it as a "floodplain" area as the tide goes in and out. In the park, it was mostly filled with Juncus roemerianus (black needlerush). At the edge of the marsh, the treeline pretty much just starts up suddenly where the highest reaches of saltwater ends.


The standard southeastern maritime forest is fairly open with trees spaced far apart (that is, you can see pretty far into it and it's easy to walk through). The tallest are pines, but there's a variety of deciduous and palm-type trees in the midlevels. Saw palmettos stand out as the main part of the understory. The pines have extra-thick bark and there's lots of pine needle litter, which means fire is a part of the ecology.


Far enough inland away from the saltwater, there are shallow freshwater ponds. Some of which are called "sloughs" (sloo). These are a type of wetland. Also, in places where spanish moss is especially thick, the distant forest can look ghostly silvered.

All in all, I walked about 7 miles and saw every part of every trail (almost... would've gotten the last bit too if my legs hadn't wore out). Skidaway Island State Park isn't that big and can easily be seen all in one day. The trails are all flat and wide (would rate "level 1 difficulty"), but then, coastal Georgia is pretty flat. And it turned out to be a good idea to wear my crocs for the venture because I had to wade through some of it (it rained a lot over the weekend).

Some boxplots about baby fish

It's been a while since I've said anything sciencey here because, well, being laid off from my sciencey day job has kind of drastically reduced (possibly even eliminated) the number of sciencey things I do on a daily basis. However, all is not lost! I can still dig up past sciencey things I've done, such as for my masters thesis. :)

To the right are some pictures of baby fish - five species of Lutjanus snappers that usually live in Florida but had gotten lost in North Carolina at the time they were caught. They were about 1-2 cm long at the time. We caught hundreds of them, mostly L. griseus, during two (non-consecutive) years of sampling with nets. Among other things, we compared their size ranges with each other:

These are box plots. Which is a fun modern statistical way of looking at data besides just getting an average and a standard error or standard deviation (also included, because older scientists who aren't used to fun modern ways prefer to see those there). As you can see, some of them came in bigger than others. :)

This post inspired by Janiece, who is learning about box plots in her statistics class.

Freelance Science

Now that I have three whole articles up at Bright Hub, I thought I'd mention it here. :) Bright Hub is basically a collection of science and technology articles. The pay is potentially better than eHow (we'll see if that's true in a few months), and they have actual quality control in the form of editors who approve article ideas before they're written, and then approve the articles again before they're published. (eHow's idea of quality control is to delete stuff after they've been published, without telling anyone, and without sending back the stuff they've deleted. -.- Though they're slowly getting better about informing people.)

So far I'm enjoying writing for them. Compared to eHow, the possible topics I can write about are more in line with what I can actually write about, and the format is more flexible. I have lots of ideas for future articles, mostly about ecology and evolution and marine science, but I'm hoping to have a variety to show off as samples for more lucrative writing work later on.

Thanks to fellow UCFer Jeri for pointing me to the place. :)

A weird little geological bowl

This cliff is part of a rocky beach somewhere in southern California. Notice how there's a dark-colored band of rock that winds around the bottom, like a bowl, that there's more tightly folded light-colored rock in the bowl, and there's a big crack down the middle (with the trees growing in it) that doesn't seem to go through the bottom of the bowl.

My first thought was that the crack is a fault. The light-colored rocks on either side of it don't appear to meet up with each other. However, because the dark-colored band is continuous along the bottom, it might be a dike that just weathered faster than the surrounding rock.

Which is not to say that there aren't faults in this picture. To the right of the bowl, some of the light-colored rock is doing some interesting folding action, and in one spot it comes to an end against another band of the same stuff.

All in all, a fun little head-turner for the casual roadside geologist. ;)

As for where it is, I hope someone out there can tell me. The picture was taken in December 1994, and is of the same place as these:


I was there with some extended family during a two-week visit, my first trip to California, and they were showing us around.

I mention all this now because I just found the original photos while excavating my storeroom, and was rescanning Crash of Waves for a friend to turn into art.

A Faulted Dike

In geology, a bedding plane is where sediments settled over a really long time and turned into layers of rock, with the oldest at the bottom and youngest at the top. Sometimes after this happens, the land shifts around so that the bedding plane isn't horizontal anymore, but might be tilted at an angle, or folded in curvy patterns.

A dike or sill is when a finger of molten rock penetrates through regular cooled, hard rock. If it's going in the same direction as the bedding plane, it's a sill. If it cuts across several of them, it's a dike.

A fault is when there's a really big crack that turns a bedding plane into two pieces, and one piece shifts position relative to the other piece.

And this:




is the sort of sight that would make your average roadside geologist swerve off the road while staring in fascination. That's a dike (or sill) that got cracked up into fragments. It's next to the Hoover Dam in Nevada/Arizona, where the land looks like it went through so much violent upheaval that there's no bedding plane at all anymore, it's all been crinkled into rubble. I imagine it's great fun trying to piece together what happened, and how, and in what order.


Note: I was on foot. No motorists or pedestrians were harmed in the taking of this picture. Also: click on the picture to get the full effect of its scale; those metal things at the top are electricity towers.

Summary of the Debunking of a Crank

So. There's this brand new shiny particle accelerator in Geneva, known as the Large Hadron Collider. There are also some concerned citizens who think that it might make black holes that will destroy the Earth. Two of these, Luis Sancho and Walter L. Wagner, filed for a restraining order against it in a court in Hawaii (note: Hawaii is nowhere near Geneva). It got tossed out of that court recently, but rumor has it that they're planning to file an appeal.

On what grounds is Mr. Wagner making these claims about black holes? How does he know? Well, he says he's a nuclear physicist. After a lengthy foray into researching his credentials over at John the Scientist's blog, however, it has become rather clear that he's not. The discussion there is longwinded and goes around in great big circles, so I'm making a clear summary of it here. Specifically, let's go line by line through the affidavit he filed with his restraining order in Hawaii...

AFFIDAVIT OF WALTER L. WAGNER IN SUPPORT OF TRO AND PRELIMINARY INJUNCTION

I, Walter L. Wagner, affirm state and declare, under penalty of perjury of the laws of the State of Hawaii, as follows:

1. I am a nuclear physicist with extensive training in the field. I obtained my undergraduate degree in 1972 at Berkeley, California in the biological sciences with a physics minor, and graduate degree in 1978 in Sacramento, California in law.

a) The second sentence actually contradicts the first. "Physics minor" != "extensive training in the field of nuclear physics."
b) It turns out that his law degree is a JD, not a PhD, and it's from an unaccredited institution, the University of Northern California Lorenzo Patiño School of Law. Not only isn't he a nuclear physicist, he's also not a lawyer. He is not and has never been a member of the California Bar, the Hawaii Bar, and probably not any other state bars either.
c) His only actual degree is a BA in biology. (We think. So far we've not had reason to check whether he has even that...)
d) Despite the fact that he calls himself "Dr." everywhere, he doesn't actually have any right to claim that title.

2. Commencing in 1973 I worked extensively in cosmic radiation research at UC Berkeley, Physics Department, Space-Sciences, and am credited with discovery of a novel particle only previously theorized to exist [by Nobelist P.A.M. Dirac], namely a magnetic monopole. That discovery still remains controversial as to the identify of that novel particle, and numerous searches for magnetic monopoles are still currently underway, or proposed, including at the Large Hadron Collider [LHC].

a) The scientists who published the 1975 paper claiming it to be a magnetic monopole later retracted their claim in a 1978 paper.
b) He was a lowly lab tech that was hired to be a scanner. He was told what to look for by the real scientists, and had no part in the actual scientific conversation surrounding the unexplained particle. This is borne out by examining the authorship and acknowledgements of the papers in question. When he says "credited with", what he means is "mentioned in the acknowledgements for assistance." He also fails to mention that he wasn't the only hired scanner in the lab at the time.
c) Nowadays the discovery is viewed as a historical curiosity, not a controversy.

3. Commencing in 1979 I began employment as a federal nuclear safety officer with the US government, from which I am currently retired, though I remain in frequent contact with my former duty station. My federal duty station was with the US Veterans Administration, and I managed an extensive program of nuclear safety involving usages of ionizing radiations from machines [X-ray, CT, etc.], and from a wide variety of radioactive materials produced by particle accelerators, in nuclear reactors, or extracted from nature [principally uranium and its radio-daughter radium]. This work involved enforcement of the regulations of the US Nuclear Regulatory Commission, the US Department of Energy, and the US Department of Transportation. Essentially, my job was to look for and root-out the safety flaws overlooked by scientific researchers as it pertained to nuclear physics, as a protection not only for the researcher’s own health, but for the visitors and population at large.

a) A nuclear radiation safety officer is a type of lab tech and bureaucrat. They do some simple labwork and lots of paperwork overseeing safety regulations. They don't do nuclear physics or any other kind of science.
b) They don't practice nuclear medicine, either. Not even if the job in question is in a hospital.

4. Following retirement from federal employment I embarked on teaching science and mathematics for many years to grade school and college students. I was noted for having obtained the highest test-score on the basic teacher credentialing examination in California [CBEST] where I initially began teaching. I am presently likewise retired from that field, though I still engage myself in formal programs for science education, including the Journey Through the Universe educational outreach program hosted annually by the Big Island astronomy community, where I live. Such
educational endeavors included periods of time as an instructor at Punahou, Iolani, and several other schools in the Honolulu district.

a) He successfully passed a standardized test for grade school teachers. (This, also, does not make him a nuclear physicist.)
b) Educational outreach likewise does not make one a nuclear physicist. A bachelors degree in biology would qualify him for the stuff he mentions.

5. I have remained active in the field of theoretical nuclear physics, and serve as a science editor for Wikipedia, having numerous articles and revisions in nuclear physics to my credit, and I am very familiar with the editing procedures and processes, and with the nuclear physics editors at Wikipedia. I have been active in the field of theoretical micro-black-holes being created by advanced colliders since publication of my work in Scientific American in July, 1999.

a) Becoming an editor at Wikipedia is approximately as difficult as becoming a member of Myspace. Signup is an automated process of choosing a name and password. Anyone can sign up and edit anything, and if they're sneaky about making themselves look authoritative and intelligent, they can insert all kinds of spurious, wildly inaccurate claims that go unchallenged for a very long time. This is why Wikipedia is not highly regarded as a citable source for in-depth information.
b) His claim for being active in the field of "theoretical micro-black-holes being created by advanced colliders"-ology appears to be based on the educational outreach mentioned in 4.
c) Scientific American is not a peer reviewed scientific journal.
d) His "publication" in it in July 1999 was a letter to the editor.

After two weeks of arguing with Wagner and his faithful minions, the general consensus among the UCF is that the man is mentally defective, possibly clinically insane.

As for the other guy, Luis Sancho, it doesn't take much of a look at all at his website to know where his sanity stands. If he was worldbuilding for some kind of cyberpunk story with sentient AIs in an alternate universe, that would be a great site, but, uhhh. I think that's all anyone really needs to say about that.

Meanwhile, has the Large Hadron Collider destroyed the world yet? Click here to check on the status of that.

Update: courtesy of Nathan, there's also this bit of excellently useful data:

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One final note. Comments on this post will be heavily moderated because I don't want the arguments to wander over here, too. This article is meant to clarify things, not make everything all muddy. John is the official host of this particular circus, if you want to say something significantly in disagreement, do it over there. I will update this as things continue to progress at Refugees.

Open House 2008

Every year, the institute where I work has an Open House, wherein we let the general public mob the place. Allegedly they're there to learn what the institute does to deserve taxpayer money, and maybe some basic marine science too. In practice it's more a place for small children to get their faces painted and do crafts and run races and play inside a giant inflatable whale. We have a jazz band, and in some years people walking around in costumes of marine creatures (and from Spongebob Squarepants).

Even so, every year we try. This year I made a poster:


(click to read)
It was as dumbed down as I could get away with. The institute faculty don't seem to know how to explain things to the average carnival-minded layperson of casual non-interest, and the other posters were pretty technical. Mine had people standing in front of it longer than the others, so I call it a success. :)

Deep End Geometry Revisited

(Note to Nathan: It's math again, but this time with no numbers at all! Only pictures! If it still doesn't make sense, well, the pictures are pretty....)


This is the type of picture I've been making for the past three weeks. That rainbow blob thing in the middle is made up of several thousand dots¹. Wouldn't it be nice if I could stretch them out to fill the whole box instead of having them all jammed together in the middle?


Here's the direction I want to stretch them. The one on the right is a bird's eye view of the same thing. Unfortunately, I can't stretch them out that way. I can only stretch them in one of these ways:


Obviously, then, I should move the blob until it's pointing in a better direction. To be able to stretch them the way I want, it needs to be pointed like so:

See how easy that was in Photostudio? Unfortunately, it doesn't work like that when it's a bunch of dots on a grid. To do what I want, I need to either move the grid around to match the blob, or move the blob around to match the grid.

Lots of people made lots of suggestions, all of which had strange side effects, so in the end, I didn't end up using any of them. See, it turns out that although it's hard to rotate a blob of dots when you have them in a box, it's not at all hard when you've got them on a circle². In fact, it's ridiculously easy.


Yep. That's what I call thinking outside the box. :) And it allows me to do this:

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Footnotes for the advanced class:

1. 79,744 total data points. Which needed to be rotated 55 degrees counterclockwise.

2. Cartesian coordinates are X, Y, Z. Polar coordinates are directions with magnitudes (or angles with radii) (or, in 3D, it's azimuth and elevation to go with the radii). Rotating in polar is easy because all you do is add to the angle. So I converted from cartesian to polar, did some addition, and then converted from polar back to cartesian. Voila!

Global Warming Worldbuilding

From Jeri (via Eric):

I need some sort of event that will cause immediate global warming in the course of one summer/fall - to the point that it will not freeze come winter in the arctic and it will happen so fast it will surprise the world. What sort of event can you think of, outside of deus ex machina?

Umm. What kind of story is this? You could always blame it on space aliens with superior technology.

Barring that, basically you'd have to find a way to dump a whole lot of carbon dioxide into the atmosphere. A whole lot. Enough to overwhelm all the balances that are presently in place.

I used to have a book, Out of Thin Air by Peter Ward, that explained how the Mesozoic got to be as warm as it did. I no longer have it, so going entirely by memory here, but basically it was because all the accumulated plant detritus during the Carboniferous (which was called that for a reason...) suddenly released their stored carbon into the atmosphere. I think he said it was a really big fire.

So... maybe in your case, find a way to burn every single plant in the entire world?

Translating Geology into English

The abstract of a recent geology paper, Dating the First Stage of Planet Formation, says:

The Mn-Cr chronometer applied to bulk carbonaceous chondrites constrains the solar nebula volatile element fractionation, chondrule formation, and stage I planetary accretion timescale to within +0.91 to -1.17 Myr at 4568 Myr ago. The difference between the initial 53Cr/ 52Cr ratio of ordinary chondrites, defined by Chainpur (LL3.4) chondrules, and carbonaceous chondrites suggests that the former is coming from an isotopically evolved reservoir.

In English, what they said was:

The solar system first began to form about 4.568 billion years ago, though it could've been as much as 0.91 million years more than that, or 1.17 million years less than that. They figured this out by using the Manganese-Chromium dating method on some meteorites (rocks from space) known as chondrites. This is like the carbon dating method, except with manganese and chromium. It's done in a chemistry lab.

How this works: The chromium atom has 24 protons and also a bunch of neutrons. 53 Cr is a chromium atom that has 29 neutrons, and 52 Cr has 28 neutrons. 53 Cr and 52 Cr are called isotopes of chromium. A rock, when it first forms from moltenness, will start out with a certain amount of 53 Cr. As time goes by, the 53 Cr will gradually turn into 52 Cr through radioactive decay. By measuring how much of each type is in the rock (a ratio), it's possible to get a good estimate on how much time has gone by since it first formed.

The authors of the paper did all this on a special type of chondrite (the carbonaceous kind), and by looking at it, they think that the regular kind of chondrite started out from a pool of moltenness that had already done some radioactive decaying before cooling into rocks.

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I've read a lot of science papers from all of the main branches of science, and I must say that geologists are by far the grand prize winners when it comes to obfuscatory writing. This is to hide the fact that geology is really so easy to understand that anyone could do it if it was explained clearly to them. I've seen 15-20 page papers, chock full of really big words and dense grammatical structures, that could've been written in 5. Since grant funds tend not to be justified if you only write a few paragraphs to explain what you did, though, professional geologists have to make what they do look bigger and more complicated than it really is.

The above was translated off the top of my head at the request of someone in a chat channel. I felt like putting it here, too, to make me feel smart - as a counter to yesterday's post which makes me feel like a failure. The only thing I looked up was how many protons chromium has. Therefore, take my accuracy with a grain of salt. ;)

My favorite kind of warning sign

Seen on the office door of one of the faculty:
(click to read.)

One of the biggest hazards of doing science in the field is tampering and theft by random passersby. It never helps to explain anything in the hopes that people will just nod along and leave things alone. Trickery and camouflage tend to work better. When I was in grad school helping a fellow student do some research with shorebirds, they had a box of tracking equipment that had to just sit out in the middle of an island. It was surrounded by a useless but official looking fence and plastered with "Warning: High Voltage" signs. Seemed to work pretty well.

And perhaps humor works well too. ;) The above sign, which is probably also out in the field attached to some electronic equipment too heavy to steal, reminds me of the birdwatcher's box.

What water temperature looks like from orbit

This is what sea surface temperature looks like off the coast of the southeastern U.S. in the fall, as seen from space. The scalebar is in Celsius. Those +'s are a grid of U.S. Navy towers that used to be for flight training. We have sensors at the ones with squares. The red streamer is the Gulf Stream, which is a stream of warm water that comes from the Gulf of Mexico and goes in an enormous clockwise circle in the northern half of the Atlantic Ocean. While it's doing that, it moves a lot of fish around and keeps England warm.

Making this sort of picture is approximately half my job description (other half being that ton of cruise data that I've been banging together a SQL database for in the past several months). I also make them for chlorophyll levels, dissolved organic matter, light penetration, and a number of other more arcane things. It's fairly mindless work compared to learning how to code things, and the results are pretty.

Open House Weekend

"This is the boat's dry lab. Over there is the wet lab. This is where we do all the science on the boat. Different groups of scientists will bring their own equipment on board. The dry lab is where they put all the electronics equipment and computers. The wet lab is for anything to do with seawater samples or chemicals. The idea is to keep them separate from each other.

"Over here we have the computer that controls the equipment out on deck. See that circular looking thing right outside the door? This computer controls that. As we put it overboard and send it down to the bottom of the ocean, we can watch the data come in in realtime on the display. Also, all those tube things are water bottles. When we send it down, they're open at both ends - and when we see some water we want to collect, we can push some buttons on this rack over here, and it'll close up, so we have a sample at the depth we want.

"That display tells us how deep the water is where we are now. It's coming down from the bridge. That's a giant magnifying glass with a light. Those are immersion suits, which are for if the boat sinks. That's just the eyewash. No, they don't actually let me go out on the cruises. I know nothing about global warming, quit trying to make me say something authoritative."

... is what I did for four hours yesterday.

"Sometimes you have to lose some money to keep the customer. We could've either given him the $25 that the former manager owed him, so that he would keep coming back to buy food and therefore give us more money in the future, or we could make him pay the entire amount for his food now and never see him again. I see we've chosen the latter, and now we'll argue about it for my entire shift."

... was the three hours after that.

"braaaaaiiinnnsss....."

... was the rest of my day.

As for today:

I'm 34.

Mmm... sushi.

So ... what do marine scientists do while sailing the high seas?

(more info about the video plus a download link)

This is a montage of photos and videos taken from research cruises in New Hampshire. The whole thing is set to Ice, Ice, Baby. I've done virtually everything mentioned in it at some point or another. :)

How to have a well-run research cruise

1. First, it's good to remember to take your station logbook with you, so you can remember to write down important basic info about each station. Like, where it was, what day it was, what time, how deep the water was, etc. Ideally this should be written on sheets of paper with preprinted forms on them, and not a wad of sticky notes.

2. Having a station logbook also helps you avoid giving more than one station the same number.

3. Not to mention it probably helps remind you that stations ought to have numbers in the first place, or at least some kind of distinct name.

4. A cruise plan is good too. That way you don't have to go back to previous stations because you forgot to do something.

5. Second, a CTD depth profile is not actually supposed to be a race to the bottom. You really do want the instruments to take more than one measurement per meter or two.

6. Additionally, if you're hoping to have any useful data from the top 1.0 meters, try to do the CTD presoak shallower than 1.5 meters.

7. Yes, it turns out that the presoak actually is a requirement. Remember: not a race.

8. Third, the time to discover that some of the sensor calibrations are on crack should not be while the cruise is underway.

9. Fourth, it's helpful to have all of the equipment on the boat recording time in the same time zone.

10. And finally, remember that water never has a density of -2.


p.s. Not related to actual cruises, just to the data workup afterward: be aware that all of your Matlab pre-7 scripts will break in Matlab 7 in astoundingly stupid ways.