The joyous first week begins

Things are back to usual here at Rhosgobel, as classes have started again; I just met my lecture students for the first time today. I was asked many spontaneous questions during the lecture; all of them were relevant to the topic at hand, and some were quite advanced. I couldn't have asked for a better first lecture.

It's been an interesting past few months; back in October our spring schedule was cut by a large fraction for budgetary reasons, but in the past few weeks the administration has realized that enrollment is now way down (gee, never would have expected that ...), and thus the administration has been frantically asking us to add lab sections. Adding labs at the last minute is an administrative disaster, as we have to find adjuncts to teach the labs, arrange for lab techs to support the labs, order supplies to teach the labs, and find timeslots to fit the labs in (oh yes, and notify the students that the new lab exists). My department has pulled through amazingly and added four new labs, two of them just in the past week. I'm so proud!

Other administrative headaches are also piling up and distracting me from teaching. Probably the largest is that the administration already wants both next summer's and next fall's schedules drafted out within the next few weeks. The fun never ends!

Why is this only being reported now?

CNN's big headline this morning read "FEMA's big kiss-off?"; it was positioned above a picture of a stranded Katrina victim captioned "Some loss of life 'might not have occurred,' senator says."

While I appreciate that CNN is covering the story about turned-away Katrina aid, it makes me wonder why that headline and provocative quote weren't present in the weeks after the hurricane (when, for instance, I was able to easily collect more than 20 unique reports of denied Katrina aid; see this post for the full list).

The CNN article appears to have been spurred by the investigations of a congressional committee into the response to hurricane Katrina (the committee is summarized here, and its hearings are detailed here). The CNN article does have some new information in it; for instance, the committee has uncovered evidence that FEMA even rejected offers of aid that came from within the US government.

The Interior Department offered FEMA 500 rooms, 119 pieces of heavy equipment, 300 dump trucks and other vehicles, 300 boats, 11 aircraft and 400 law enforcement officers, according to a questionnaire answered by a department official.

Interior law enforcement officers included special agents and refuge officers from the department's Fish and Wildlife Service.

"Although we attempted to provide these assets, we were unable to efficiently integrate and deploy these resources," an Interior Department official wrote the Senate committee investigating the government's response to Katrina.

...

[Within three days of the hurricane landing,] the Interior Department had offered FEMA hundreds of law enforcement officers trained in search-and-rescue, emergency medical services and evacuation, according to the documents.

"The Department of the Interior was not called upon to assist until late September," the Interior official writes.

The hurricane made landfall on August 29.

The chair of the investigatory panel (Senator Susan Collins) seems to be (understandably) outraged:

"Now, you might be able to understand if it came from outside government," she said. "But this is another federal agency, an agency that was offering trained personnel and exactly the assets that the federal government needed to assist in the search-and-rescue operations."

Circuses of the spineless

PZ Myers has posted two versions of the Circus of the Spineless: the first is the (more traditional) biological version, and the second is a special Senate version.

A bit of advance notice might have been useful ...

While reading Orac this morning I discovered that today was "International Internet-free Day". Well, so much for that idea.

An imprecise watch

BoingBoing has a summary of a very snazzy idea: a watch that displays time in imprecise units like "Around 6 Fifteen" and "Just Before 7". Apparently you can get a plugin to do this on your Mac menubar; I wonder if there's a Gnome/X-windows plugin for it.

Kerry's speech on Alito

Last night on CSPAN (yes, I've taken to watching CSPAN), I watched most of John Kerry's speech on why he's filibustering Alito; the speech was well-delivered and information-rich, and the full text is available online. Here's an excerpt:

"In 1984, for example, Judge Alito wrote a Justice Department memorandum concluding that the use of deadly force against a fleeing unarmed suspect did not violate the fourth amendment. The victim was a 15-year-old African American. He was 5 foot 4. He weighed 100 to 110 pounds. This unarmed eighth grader was attempting to jump a fence with a stolen purse containing $10 when he was shot in the back of the head in order to prevent escape. The Sixth Circuit Court of Appeals found the shooting unconstitutional because deadly force can only be used when there is 'probable cause that the suspect poses a threat to the safety of the officers or a danger to the community if left at large.' That is what we teach law enforcement officials.

"But Judge Alito disagreed. Judge Alito said: No, he believed the shooting was reasonable because 'the State is justified in using whatever force is necessary to enforce its laws'--even deadly force. That is his conclusion. That is the standard that is going to go to the Supreme Court if ratified. It is OK to shoot a 15-year-old, 110 pounds, a 5-foot-4-inch kid who is trying to get over a fence with a purse, shoot him in the back of the head.

...

"Perhaps Professor Liu of the Berkeley Law School put it best when he wrote this. He said:

'Judge Alito's record envisions an America where police may shoot and kill an unarmed boy to stop him from running away with a stolen purse; where federal agents may point guns at ordinary citizens during a raid, even after no sign of resistance; where the FBI may install a camera where you sleep on the promise that they won't turn it on unless an informant is in the room; where a black man may be sentenced to death by an all-white jury for killing a white man, absent a multiple regression analysis showing discrimination; and where police may search what a warrant permits, and then some. This is not the America we know. Nor is it the America we aspire to be.'"

Google China

Much media hay was made of Google's recent decision to launch google.cn, a Chinese version of their search engine that censors (or, in Google's terminology, "filters") search results. Today Google posted a detailed article outlining their reasoning for bowing to Chinese censorship. Of note is a part of the story that isn't being reported heavily:

... Chinese regulations will require us to remove some sensitive information from our search results. When we do so, we'll disclose this to users, just as we already do in those rare instances where we alter results in order to comply with local laws in France, Germany and the U.S.

As an example, the search results for "tiananmen" are drastically different in the Chinese and English versions, but there appears to be text at the bottom of the Chinese page that indicates the search has been censored (babelfish translates the text as "According to the local law laws and regulations and the policy, the part searches the result not to demonstrate. You are not must look: Tiananmen").

It'll be interesting to hear what Semantic Compositions has to say on the topic, as he's previously talked about Google's censorship of US search results.

You know blogs are big when ...

... the source the New York Times uses to report that a senator (John Kerry) has called for a filibuster is that senator's personal post on a blog (Daily Kos; Kerry's post can be found here).

The issue, of course, is the confirmation hearing of proposed Supreme Court justice Samuel Alito; see this New York Times editorial for why some might want to fillibuster Alito.

Surveilling Americans

The ACLU of Georgia has filed a lawsuit alleging that the government has been secretly surveilling peaceful protests. The lawsuit is based on the questionable arrest of two activists after they wrote down the license plate number of an undercover Homeland Security agent taking pictures of the protest. WXIA news has a story on the suit:

Two documents relating to anti-war and anti-government protests, and a vegan rally, prove the agencies have been "spying" on Georgia residents unconstitutionally, the ACLU said. (Related: ACLU Complaint -- PDF file)

For example, more than two dozen government surveillance photographs show 22-year-old Caitlin Childs of Atlanta, a strict vegetarian, and other vegans picketing against meat eating, in December 2003. They staged their protest outside a HoneyBaked Ham store on Buford Highway in DeKalb County.

An undercover DeKalb County Homeland Security detective was assigned to conduct surveillance of the protest and the protestors, and take the photographs. The detective arrested Childs and another protester after he saw Childs approach him and write down, on a piece of paper, the license plate number of his unmarked government car.

...

The government file lists anti-war protesters in Atlanta as threats, the ACLU said. The ACLU of Georgia accuses the Bush administration of labeling those who disagree with its policy as disloyal Americans.

The ACLU has the full text (PDF) of its complaint online; it contains a detailed narrative of the events surrounding Childs' arrest (starting on page 6).

Ah, satire

Fafblog has recently posted two good satirical pieces; the first is an explanation of recent Democratic party behavior, and the second is a Q&A session about Bush's NSA wiretapping program. I'll steal BoingBoing's quote from the second article as a small sample of what awaits on the other side of the links:

Q. ... But is it legal for the president to ignore the law?
A. Maybe not according to plain ol stupid ol regular law, but we're at war! You don't go to war with regular laws, which are made outta red tape and bureaucracy and Neville Chamberlain. You go to war with great big strapping War Laws made outta tanks and cold hard steel and the American Fightin Man and WAR, KABOOOOOOM!
Q. How does a War Bill become a War Law?
A. It all begins with the president, who submits a bill to the president. If a majority of both the president and the president approve the bill, then it passes on to the president, who may veto it or sign it into law. And even then the president can override himself with a two-thirds vote.

What is this, wake up Radagast and SO early month?

Two weeks ago it was collapsing shelves. Today it's someone using a sledgehammer to knock down our fence. Before 8am. Very loudly.

You'd think we'd be expecting something like that, what with our fence falling down last year and us hiring a contractor to replace it. And you'd be right, except that we were expecting our contractor to show up tomorrow. Not today.

After groggily wandering out into the backyard (and deciding that "What the *$#@ are you doing on my property?" was probably not the best way to start a conversation), I found out that our contractor neighbor had just decided to get things started early. Oh yay. So much for sleeping in.

Something fun

OK, after the last three posts we need something fun here, and thanks to BoingBoing I've got just the thing: Business 2.0's list of the 101 dumbest moments in business of 2005. They also have a (much shorter) list of the smartest business decisions (which can be found via the previous link).

Iraq reconstruction

The LA Times and New York Times both have articles showing that the reconstruction of Iraq is not proceeding as planned. The LA Times reports that oil production in Iraq (which was intended by the US to help fund reconstruction) has decreased:

Iraqi oil production fell by 8 percent last year, with a sharp decline near year's end that left average daily production at half the 3 million barrels envisioned by U.S. officials at the outset of the war in 2003.

Prospects for improvement this year are slim, according to many experts, calling into question Iraq's ability to support itself and fund reconstruction efforts as U.S. assistance is scaled back. Reasons for the shortfall include the poor state of the nation's oil fields, a creaky infrastructure, poor management and ongoing insurgent attacks, particularly to pipelines in the north-central region meant to export oil through Turkey.

...

Oil revenues contribute 94 percent of the fledgling government's budget and a drop in oil global prices from current high levels could wreak havoc if output remains depressed.

The New York Times reports on an audit by the military's Special Inspector General for Iraq Reconstruction (SIGIR) into use of Iraq reconstruction funds:

A new audit of American financial practices in Iraq has uncovered irregularities including millions of reconstruction dollars stuffed casually into footlockers and filing cabinets, an American soldier in the Philippines who gambled away cash belonging to Iraq, and three Iraqis who plunged to their deaths in a rebuilt hospital elevator that had been improperly certified as safe.

...

Agents from the inspector general's office found that the living and working quarters of American occupation officials were awash in shrink-wrapped stacks of $100 bills, colloquially known as bricks.

One official kept $2 million in a bathroom safe, another more than half a million dollars in an unlocked footlocker. One contractor received more than $100,000 to completely refurbish an Olympic pool but only polished the pumps; even so, local American officials certified the work as completed. More than 2,000 contracts ranging in value from a few thousand dollars to more than half a million, some $88 million in all, were examined by agents from the inspector general's office. The report says that in some cases the agents found clear indications of potential fraud and that investigations into those cases are continuing.

...

[T]he portrait it [the audit] paints of abandoned rebuilding projects, nonexistent paperwork and cash routinely taken from the main vault in Hilla without even a log to keep track of the transactions is likely to raise major new questions about how the provisional authority did its business and accounted for huge expenditures of Iraqi and American money.

...

Sometimes the consequences of such loose controls were deadly. A contract for $662,800 in civil, electrical, and mechanical work to rehabilitate the Hilla General Hospital was paid in full by an American official in June 2004 even though the work was not finished, the report says. But instead of replacing a central elevator bank, as called for in the scope of work, the contractor tinkered with an unsuccessful rehabilitation.

For the full-text of the SIGIR audit mentioned in this article, as well as many other SIGIR audits, see this page.

Katrina: investigations hindered and water wasted

Now that I'm back from vacation, it's time to catch up on my political reading. First on my list was catching up on hurricane Katrina news. The New York Times reports that the Bush administration is hindering a Congressional investigation into the response to the hurricane:

The Bush administration, citing the confidentiality of executive branch communications, said Tuesday that it did not plan to turn over certain documents about Hurricane Katrina or make senior White House officials available for sworn testimony before two Congressional committees investigating the storm response.

...

"There has been a near total lack of cooperation that has made it impossible, in my opinion, for us to do the thorough investigation that we have a responsibility to do," Senator Joseph I. Lieberman, Democrat of Connecticut, said at Tuesday's hearing of the Senate committee investigating the response. His spokeswoman said he would ask for a subpoena for documents and testimony if the White House did not comply.

...

[E]ven Senator Susan Collins, Republican of Maine, objected when administration officials who were not part of the president's staff said they could not testify about communications with the White House.

"I completely disagree with that practice," Ms. Collins, chairwoman of the Senate Homeland Security and Governmental Affairs Committee, said in an interview Tuesday.

According to Mr. Lieberman, Michael D. Brown, the former director of the Federal Emergency Management Agency, cited such a restriction on Monday, as agency lawyers had advised him not to say whether he had spoken to President Bush or Vice President Dick Cheney or to comment on the substance of any conversations with any other high-level White House officials.

And, to keep adding to the list of unused aid, the USA Today reported a few weeks ago:

One million cans of drinking water donated for hurricane relief have been emptied and recycled because the water was never used at Texas and Louisiana hurricane shelters, the Federal Emergency Management Agency said.

FEMA hauled the 400,000 liters of water, or 18 truckloads, to a scrap metal business in the Dallas area last month. The water was dumped into a sewer and the cans sent for recycling.

The joys of being department chair

Normally the week before the semester starts is a relatively peaceful one: no students are on campus, and I typically work at home at my own pace. However, on returning from my trip I had two phone messages at home and dozens of e-mails, most of them relating to my role as department chair. The administration has decided it wants to add some classes at the last minute; the department has already found the adjuncts required to do it, but I've got to make sure all of our (already overworked) techs get paid for the extra work they'll be required to do. Also on my schedule for this week is preparing to fight to get a replacement position for a faculty member who's leaving, and trying to figure out how to pay for an unexpected multi-thousand dollar repair bill.

Oh yes, and sometime I should get ready for my courses ...

I'm back!

While my SO and I enjoyed our trip, our house is now filled with many contented sighs as we're both happy to be back home. The trip had lots of fun little tidbits, including:

• Staying with church friends of my mom in upstate New York; we were initially very hesitant to stay with complete strangers, but they ended up being among the nicest people we know. Both were in their 80s (yet are more active than we are), and were great fun to chat with over the breakfasts they kindly made for us each morning.
  
• Once again meeting my great aunt via a trip that entailed both of us traveling many more hours than it would take us to drive to each others' houses.
  
• Having yet more delicious food, including chicken paprikash (a favorite of ours that I've never gotten around to posting), an improvised chocolate version of baked French toast, and a tasty gathering at Buca di Beppo.
  
• Remembering why I love Firefox so much by being forced to use Internet Explorer for days on end.
• Providing a very good excuse for me to avoid reading work e-mail for a full seven days.
  
• And finally, an event that should make PZ proud: we experienced an upstate New York snow storm (~5.5" in one day), and were wandering around in 25F weather many nights on our way back to our lodging. Hats, scarves, gloves, and jackets were worn regularly!

I'll return to regular posting tomorrow; right now it's time to collapse.

It's a bug!

Really! It is! This bundle of cuteness is a hemipteran - a true bug (see this post for more on what a hemipteran is, and why this is one of the only organisms you can actually call a bug).

This is the nymph of a southern green stink bug (Nezara viridula), which I found on my tomato plants this past summer. I took the pictures way back in August, but never got around to posting them, so now that it's winter and I'm on vacation it seems like a perfect time to pull them out.


When I saw this crawling around on my tomato plants I immediately recognized it as a hemipteran, but I had no idea what species it was. After much searching I got the species ID from bugguide.net, where they have pages on hemipterans, stink bugs, and southern green stink bugs. I shouldn't have wasted my time hunting for the ID though, as Urtica posted the species ID as a comment on my Flickr page only minutes after I uploaded it. Thanks, Urtica!


As with all hemipterans, this insect has piercing mouthparts (which you can see in the picture above; the mouthpart is the brown tube reaching back from the insect's head on the underside of its body) that are used for feeding on fluids . In fact, while I was taking pictures I got to see the hemipteran use the tube to feed on a tomato leaf. These bugs feed primarily on tomatoes, and when they feed on the developing fruit of the tomato they can cause it to become disfigured:

When the young green fruit is injured, the cells at the site of feeding are killed by the toxic saliva injected by the bugs into the plant. This area of the fruit stops expanding, while the cells around the dead cells continue to expand by increasing their water content. The result is deformed fruit that appears to have dimples. This type of damage has been called "cat facing." When ripened or nearly ripened fruit is injured, the injection of toxic saliva merely kills a cluster of cells that later forms an off-color hard mass in the fruit, reducing fruit quality and producing a bad flavor to the fruit.

For more information on these bugs, see the Texas Cooperative Extension (where the quote above comes from), the University of California IPM online, and the University of Arkansas Cooperative Extension (which includes pictures of nymphs).


Oh, and if you thought that I was being taxonomically inappropriate with my magazine cover headline, I had these pictures in mind when I created it.

Ants with antibiotics and herbicides

One of the fun biology facts I love to introduce in my biology classes is that humans weren't the first species to develop farming; ants began farming millions of years before our ancestors were even walking bipedally. For example, leafcutter ants (genera Atta and Acromyrmex) bring back pieces of leaves to their nest, which they then use as a medium for growing fungus; the fungus digests the cellulose in the leaves (which the ants can't do alone), and then the ants eat the fungus. The ants even bring fungal spores with them when they start a new nest.

I've known for a while that leafcutter ants weed their fungus farms, but Scientific American's online news has a few neat stories showing that tropical ants use both antibiotics and herbicides to modify their environment.

Some ants rear a type of bacteria that kills other bacteria:

Entomologist Cameron Currie of the University of Wisconsin and his colleagues discovered the antibiotic bacteria in crescent-shaped pits on the exoskeletons of two species of Panamanian ants, Cyphomyrex longiscapus and C. muelleri, after scanning them with an electron microscope. The bacteria--of the Pseudonocarida genus--bloom on the individual face plates and other exterior parts of the ant, allowing it to rub the antiparasitic agent on its fungi crop. The ant also nurtures the microbe by secreting nutrients from special exocrine glands connected to the shallow pits.

And some ants use formic acid as an herbicide:

Sections of the rainforest made-up almost entirely of the tree species Duroia hirsuta, are called "Devil's gardens." Local legend holds that they were produced by an evil forest spirit, report Megan E. Frederickson of Stanford University and her colleagues. But the results of a four-year field study reveal that ants that make their nests in D. hirsuta are the driving force between the homogeneous plots of vegetation. The team introduced saplings of another common Amazonia tree to "Devil's gardens," using a barrier to protect some of them from the ants. Those that were unprotected, however, were quickly attacked by worker ants, which injected poisonous formic acid into the leaves. Trees began to show signs of withering within 24 hours and most of the leaves were lost after five days.

Why Bush's NSA spying program is illegal

Fourteen legal scholars have written a letter to congress detailing why Bush's NSA wiretapping of US citizens without a warrant (which I've written about before) violates existing statute and is almost certainly illegal. The letter is titled "On NSA Spying: A Letter to Congress" and can be found here.

In the letter the scholars provide a lot of background on FISA and relevant Supreme Court decisions, as well as a point-by-point rebuttal of the recent Department of Justice memo (PDF) that attempted to justify the NSA spying program. The letter is well worth reading; here's the conclusion:

In conclusion, the DOJ letter fails to offer a plausible legal defense of the NSA domestic spying program. If the administration felt that FISA was insufficient, the proper course was to seek legislative amendment, as it did with other aspects of FISA in the Patriot Act, and as Congress expressly contemplated when it enacted the wartime wiretap provision in FISA. One of the crucial features of a constitutional democracy is that it is always open to the President—or anyone else—to seek to change the law. But it is also beyond dispute that, in such a democracy, the President cannot simply violate criminal laws behind closed doors because he deems them obsolete or impracticable.

A view of the trip

Last night, while watching "Wal*Mart - The High Cost of Low Price" (a good look at Wal*Mart's bad business practices, though I would have preferred the movie had stuck to presenting the facts of why Wal*Mart isn't a good company and left out some of the attempts at heart-rending stories), my SO's parents' cat decided that she wanted some of my milk:


How undignified.

I'm not going to argue with those teeth ...
Another interesting occurrence was that, on the way home from Sweet Lucy's Smokehouse (an excellent barbeque restaurant in Philadelphia) it got very cold and some white stuff began falling from the sky. The locals informed me that it was called "snow", and made up of frozen water (the craziest things happen when you leave California). After a short while it began sticking to the ground, and when I woke up this morning it was all over the place.


Snow!
The trip has been superb so far from a gastronomic perspective. On the way home from the airport (less than an hour after arriving in Philadelphia) my SO's parents stopped by their favorite local cheesesteak place and picked us up some cheesesteaks (with gooey melted American cheese and fried onions, of course) and a garlic pizza. Then it was fresh bagels the next morning, followed shortly by Memphis baby back ribs at Sweet Lucy's Smokehouse in the evening.

Baked French toast

This has been our only French toast recipe since we first made it a few years ago. Thick slices of bread are soaked overnight in a pan with brown sugar and butter on the bottom and half-and-half and eggs on top, then baked the next morning.


Pouring the half-and-half mixture onto the bread
This recipe is easier than any other French toast recipe we've seen; it does take a bit of planning ahead, but once you've sliced the bread and left it to soak overnight all you have to do is groggily pop it in the oven when you wake up, and 40 minutes later you've got hot, crispy, gooey French toast. We made this for our New Years celebration, but since I was too busy last weekend getting my lab manual ready to write a food post, this is this week's end-of-the-week recipe blogging post.


Hot out of the oven
8 tablespoons (1 stick) butter
1 cup brown sugar
2 tablespoons corn syrup (or honey)
5 eggs
1 1/2 cups half-and-half (or 1 cup milk and 1/2 cup heavy cream)
1 teaspoon vanilla extract
1/4 teaspoon salt
1 pound bread (something like French bread, challah, or ciabatta; don't use bread that has already been sliced for sandwiches)

1. Slice the bread into ~1-inch thick slices (or whatever thickness will allow you to fill a 9x13" baking pan in a single layer).
2. Heat the butter, brown sugar, and corn syrup (or honey) in a small pot over medium heat, stirring regularly, until they are combined.
3. Pour the brown sugar mixture into a 9x13" baking dish.
4. Place the bread into the baking dish, pressing it lightly into the brown sugar mixture.
4. Mix the eggs, half-and-half (or milk and cream), vanilla, and salt in a bowl, and then pour over the bread.
5. Cover and let sit overnight (8 or more hours) in the fridge.
6. Bake in a preheated 350F oven for 40 minutes, or until browned.
7. Serve immediately; we invert the slices so the brown sugar mixture is on top.

We found this recipe online years ago, and have long since lost the link to the source.

Update April 2007: Added honey as an alternate for the corn syrup.

We're off, once again

My SO and I are heading off for a week-and-a-half long trip to the east coast, our second trip of this break. The primary reason we're going back is to visit my mom (for an occasion to celebrate), but we'll also be visiting my SO's parents in Philadelphia.

I've got a few things cued up, so you can expect at least a couple of posts while I'm gone (no guarantees, though ... we might just gorge ourselves on cheesesteaks 24/7).

It's published!

My lab manual is now in print. I just ordered a copy for myself (that won't get here for at least a week), so right now I have no idea how it will look in person. It's a relief to have it done, but it's depressing to know that there are probably mistakes (since I didn't have enough time to polish it as much as I'd like). However, I'll be selling it only to my own students for at least the first year of publication, so I should have time to improve it.

Unfortunately you won't be seeing a link to the manual from here anytime soon, partially because of the limitation on sales to my own students, but also because it's published under my real name. Sorry.

Pharyngula has moved!

PZ Myers has moved to http://scienceblogs.com/pharyngula; you can read all about the details of his new site here and here.

The site is hosted by Seed, and while the new hosting agreement seems like a great deal for PZ, his host's terms & conditions (which apparently apply to PZ's work as well) seem a bit restrictive:

Except as expressly authorized by the Terms or on the Site, you may not copy, reproduce, distribute, republish, download, perform, display, post, transmit or otherwise use any of the Materials in any form or by any means, without the prior written permission of Seed Media or the respective copyright owner. Seed Media authorizes you to view and download the Materials only for personal, non-commercial use, provided that you keep intact all copyright and other proprietary notices contained in the original Materials. You may not modify or adapt the Materials in any way or otherwise use them for any public or commercial purposes.

Yikes! It sounds as though they don't even want people to post quotes from him.

[Update: It looks like Seed has changed its policy. Chris, who works with Seed, left this comment only a few hours after my original post.]

Why our prior homeowners are idiots, reasons 138 and 139

Reason 138:

My SO was awakened this morning by a lovely sound: that of our house falling apart.


Prior to 6:50am today, those shelf brackets were actually square with the wall, and supported a shelf and lots of clothes. Luckily (for me), I was already awake when the brackets decided that the wall was no longer the supportive, caring structure that it once was; unluckily (for my SO), this shelf was installed at the foot of our bed, in which my SO was still soundly sleeping. And yes, the shelves were installed by none other than our prior homeowners.

Reason 139:

We're doing a major reorganization of our garage this week, part of which entailed removing a 2'x4' section of peg board from a wall so we could move some cabinets (with the eventual goal of setting up a large garage organizer). When we removed the peg board, we found a little present:


How can one manage to install a peg board and not notice that there are car-care products still on the wall? (oh, wait, I know the answer to that ... I saw this house before our prior owners moved out)


Some owners find priceless antiques stored in their attics; we find Johnson's holiday car washing cream hidden away in our garage. Anyone have any idea what era these products date to?

New exercise plan

My SO and I now have a new exercise plan, which we've posted over on the gym. Hopefully it will give us the long-term motivation necessary to keep up exercising.

That's going to be it for today, as the lab manual needs to be in by Friday (when we leave for another trip).

Yikes!

Slashdot just linked to an article reporting that burned CD-Rs and CD-RWs have expected lifespans of only two to five years. The report has spawned lots of debates in the thread's comments (the article presents no data backing up the claim), but it does make me wonder if I should go re-burn my backups from five years ago.

Implications of the Hwang case for authorship in academia

Seoul National University released its final report (official English summary here) on the fabrication of results by discredited stem cell researcher Woo Suk Hwang. I'm not a molecular biologist, and am even further from being a specialist in stem cell research, so I'm going to refrain from attempting to summarize exactly what has happened biologically in this case. However, the case is interesting, so here's a short summary of the final report:

1) The results reported in Hwang's 2005 Science paper (Hwang WS, Roh SI, Lee BC, Kang SK, Kwon DK, et al. 2005. Patient-specific embryonic stem cells derived from human SCNT blastocysts. Science 308: 1777-1783) were completely fabricated:

The data in 2005 article including test results from DNA fingerprinting, photographs of teratoma, embryoid bodies, MHC-HLA isotype matches and karyotyping have all been fabricated. ... In conclusion, the research team of Professor Hwang does not possess patient-specific stem cell lines or any scientific bases for claiming having created one.

2) The results in Hwang's 2004 Science paper (Hwang WS, Ryu YJ, Park JH, Park ES, Lee EG, et al. 2004. Evidence of a pluripotent human embryonic stem cell line derived from a cloned blastocyst. Science 303: 1669-1674) were also entirely fabricated:

The claim in 2004 article that the DNA fingerprinting pattern of NT-1 and that of the donor A match perfectly was a clear false report. Given that none of the alleged NT-1 derived cells or tissues match the donor A, the committee concluded that NT-1 ES cell line reported in Science in 2004 is not an ES cell line derived from a cloned blastocyst. In addition, claims that photographs of cells in 2004 Science article are those of MizMedi ES cells have also been confirmed to be true. Therefore, the committee concluded that results described in 2004 Science article including DNA fingerprinting analyses and photographs of cells have also been fabricated.

3) The results in Hwang's 2005 Nature paper reporting on the cloning of a dog (Lee BC, Kim MK, Jang G, Oh HJ, Yuda F, et al. 2005. Dogs cloned from adult somatic cells. Nature 436: 641) were confirmed; the dog exists, and appears to have been cloned.

4) Not only did Hwang fabricate research, but it also appears that he used eggs donated by his junior researchers and technicians, opening questions about whether implicit or explicit coercion was involved:

Regarding the article in 2004, Professor Hwang claimed to have been unaware of the egg donation by the laboratory members. However, the graduate student who donated eggs informed the committee that the act of donation, while voluntary, was approved by Professor Hwang. Egg aspiration was carried out by Dr. Sung Il Roh on March 10 of 2003 at MizMedi Hospital, and notably, Professor Hwang accompanied the student to the hospital himself. In May of 2003, Professor Hwang's research team circulated a form asking consent for voluntary egg donation and collected signature from female technicians.

Science has a very good summary (free full-text) of how this fraud was uncovered by anonymous message board posters and journalists using somewhat unethical techniques.

One of the issues that this case brings up is how authorship on scientific papers is determined. Authorship is typically not determined by who writes the paper (though the person actually writing the text of the paper is typically an author). Instead, the list of authors is determined by who made significant contributions to the research. Often, the only contribution made by authors may have been financial or physical resources (getting grants or providing facilities), or a highly specialized technique that is relevant to only one small portion of the research (and thus the author may have no knowledge of the rest of the work in the paper). In fact, the list of authors on a paper can be determined before the research has even begun; this is often recommended so that it's clear to everyone who's getting the credit for the work (so three people don't argue at the end of the research that they should all be first author), and to encourage people to work together (the idea being that if you know you're going to be an author on a study, you'll work harder).

In theory all authors should review the final manuscript and have a say in what's written, but I have a hard time believing that papers with dozens of authors can have feedback from everyone incorporated into the paper, much less have everyone actually verify that the data were collected properly. Hwang's 2005 Science paper had 25 authors spread across multiple continents. Was it even possible that they could have verified the experimental results, especially given that one of the researchers was lying? And what happens to Hwang's 24 coauthors now that the paper has been shown to be fabricated?

Hwang is not alone in having large numbers of coauthors; the best example I know of is a landmark 2004 ocean fertilization study (Coale et al. 2004) that had 48 authors, which was then cited by another paper (Armbrust et al. 2004) that has 45 authors. Even a quick review of the Science issue Hwang's paper was published in shows that more than half of the research reports had at least five authors, and two (excluding Hwang's) had more than ten authors.

The reason why authorship is handed out so readily is that authorship is academic gold, especially in big-name publications like Science and Nature. Getting a paper in Science or Nature is a Very Big Deal; it gives you the ability to obtain funding (and get positions) you otherwise couldn't get. When there are such huge rewards for obtaining authorship, and no clear guidelines as to what constitutes a contribution sufficiently large enough to obtain authorship, it's no surprise that huge lists of authors are a reality.

Complicating the matter is that a lot of scientific writing is based on trust. To use myself an an example, all of my published papers have been coauthored with at least two other researchers, yet in all of the cases where I was the experimenter carrying out the research, I was the only one of the authors who actually saw all the raw data and analyzed it. The only thing my coauthors saw were the summary graphs I showed them, and me in the lab working hours upon hours at my experimental setups. I easily could have faked the graphs and statistics after collecting the data, and my coauthors would have had no way of knowing, short of re-analyzing tens of thousands of datapoints or redoing months of experiments (especially because, unlike Hwang, all of my experimental organisms were destroyed at the end of the study due to the data collection techniques involved). My coauthors all contributed significantly to the ideas in my papers, and thus deserved authorship, yet they had no realistic way of knowing whether I forged my data or not. So, should my coauthors be held accountable if it were found that I had forged the data?

One possible way to get around some of these issues would be to require authors to list exactly what they contributed to the paper. That way it would theoretically be clear who did what, and then if one portion of the research was found to be improperly conducted, it would be clear who should be held accountable.

Self-publishing a lab manual

About a year and a half ago, I started teaching a new lecture and lab course. I wrote most of my own labs for the course, and for the last few semesters I've been distributing the labs as handouts on my course website. This has been far from ideal, however, as the vast majority of students didn't print out the labs, and many failed to refer back to past labs, even when they were relevant to current content (as a side note, the lack of printing is probably partially my fault, as I always had extra copies of the day's lab in lab).

So, the time has finally come for me to publish my own lab manual. I looked into having the manual published by a professional science publisher, and while they were extremely willing to give me help (and many publishers came to my office to talk about the project), there were two major problems: price and flexibility. I was often quoted prices over $30 or $40 for my 250-page, black and white manual, which seemed somewhat steep (see below for comparisons). The largest problem, however, was flexibility: all the publishers would have required me to do a printing run of at least 200 or 300 copies, meaning that I wouldn't have been able to revise the manual for at least two years. Considering that I haven't had time to perfect every single lab, and there're still a few labs I'm working on writing my own versions of, I just couldn't commit to that size of a run.

So, instead of going with a professional science publisher, I'm self-publishing my lab manual. There are a number of companies that will do print on demand (POD) publishing; both Cafepress and Lulu will publish 8.5" x 11" spiral-bound black and white books. The price and minimum run size of these POD companies is near perfect: both will print the book for less than $17 per copy (students can buy the book directly through the POD company's website), and neither has a minimum run size or up-front fee.

There are some definite downsides to self-publishing a manual, however. The professional publishers all showed me huge databases of images that I could draw from; by self-publishing I'm now responsible for clearing all copyrights for all images (and other content) in the manual. Thankfully I don't need too many images, but even so, in the past two weeks I've sent out dozens of e-mails requesting permission to use various images in the manual. A relatively minor problem is that none of the POD publishers I've seen have an option to have perforated pages, which will make end-of-lab worksheets somewhat more annoying to collect (they'll have to be torn out of the manual). I'm also now responsible for all formatting of the manuscript - the only thing the POD publishers do is take a Word file and print it as-is. This means that I've just taken a crash course in publishing style guides and how to use Word professionally (thank you Google!)

Formatting the manuscript has, so far, been the most time-consuming task (other than spending the last two years writing the labs). Even though I've used Word regularly for more than ten years, I can't believe how much I didn't know. I've now learned how to use styles, the outline view, section breaks (which, for instance, let you always start a chapter on an odd page), bookmarks and cross-references (which, when combined, dynamically update links such as "see page X"), the outline view, and automatically generated tables of contents. Probably the most useful of these new skills was an understanding of styles: they've allowed me to reformat my 20+ labs into a format that is consistent throughout the book, yet is easily changeable. For instance, now that I have styles set up, I can change the font (or paragraph spacing, or bullet style, or whatever) of all the body text in my 200+ page document without changing anything about my heading, captions, or other text styles. It's amazingly convenient.

Here are a few of the many pages I've used to study up on Word; I highly recommend them:

Yes, You Can Use Microsoft Word to Set Type That Looks Professional.

Microsoft guide to styles, which links to how to apply a style and how to format a style.

The above led to how to create a template, a very useful guide to making and formatting a good Word template to start writing.

Using outline view - assuming you're using headings properly (which I am now!), learning how to use this view will save you lots and lots of time.

How to create a table of contents.

A short note on how to prevent sections of text from splitting across pages.

A summary of how to format front matter differently from the rest of the book.

Two summaries of how to do page numbering in Word.

Cafe Press guide to front matter - a great guide to what goes where.

Rhosgobel turns two!

A quick check of the archives reveals that, even though I can't possibly have been blogging for two years, the title is indeed accurate; way back on January 8, 2004 I hesitantly typed out my very first post.

The longer I blog, the more I realize that one of the joys of having a blog is that I can look back and be reminded of things I've done and been interested in. My SO will happily inform you that I often focus most of my mental energy on tasks I have yet to complete, and thus being able to look back into the past (and, say, create the 2005 Rhosgobel Index) is nice.

Of course, another benefit of blogging is the interaction I get with everyone who reads this blog, be it family, friends, or people who only know me through this site. So, I'd like to thank you, kind reader, for taking the time to visit here; it's an honor knowing that my words are read thousands of times a month.

This also seems like a good opportunity to acknowledge a person who's contributed a lot to the blog: my SO. My SO brings many interesting things to my attention and edits many of my posts (improving them exponentially).

Since last year's birthday post included my annual site statistics, it seems only appropriate to do so here. Once again I'm amazed at how many people drop by.


It's been a fun two years; I'm looking forward to the next one.

The evolution of tetrapods

The December issue of Scientific American has an excellent article by Jennifer Clack on the evolution of tetrapods (four-limbed vertebrates; aka, us). I was pondering summarizing the article here, but I just checked Scientific American's website and they've got the entire thing available for free. So, head over there and read it.

In brief, the article attempts to reconstruct the events surrounding the evolution of air-breathing tetrapod vertebrates 380 million to 375 million years ago, basing most of its conclusions on recently discovered fossils. I'll post a short bit from the article as a teaser:

With such scant clues to work from, scientists could only speculate about the nature of the transition [from fish to tetrapod]. Perhaps the best known of the scenarios produced by this guesswork was that championed by famed vertebrate paleontologist Alfred Sherwood Romer of Harvard University, who proposed in the 1950s that fish like Eusthenopteron, stranded under arid conditions, used their muscular appendages to drag themselves to a new body of water. Over time, so the idea went, those fish able to cover more ground--and thus reach ever more distant water sources--were selected for, eventually leading to the origin of true limbs. In other words, fish came out of the water before they evolved legs.

Since then, however, many more fossils documenting this transformation have come to light. These discoveries have expanded almost exponentially our understanding of this critical chapter in the history of life on earth--and turned old notions about early tetrapod evolution, diversity, biogeography and paleoecology on their heads.

Mine safety under Bush

The San Jose Mercury News reports that mine safety enforcement has been diminished during the Bush administration. While the number of "violation notices" has increased in the last few years ("in 2005 the agency issued 4 percent more violation notices for all mines than it did in 2000"), enforcement surrounding those violations appears to have decreased.

In 2001, the mine safety agency had 1,181 coal mine enforcement workers. This year, the agency had about 1,080 workers. And the president has proposed a further cut to 1,043 in the current fiscal budget.

Cutbacks in enforcement officials mean that specialists who could concentrate on the most pressing safety issues - ventilation and roof cave-ins - have been pressed into service for the routine and mandatory inspections, former officials say.

An even bigger worry, McAteer noted, is the lack of timely follow-up inspections. The problem was highlighted by a 2003 Government Accountability Office study that found that 48 percent of all citations - including the most serious ones - weren't followed up on by the mandated deadline.

This reduced staffing and lack of followup appears to be reflected in some statistics reported in the article:

The number of major fines over $10,000 has dropped by nearly 10 percent since 2001. The dollar amount of those penalties, when adjusted for inflation, has plummeted 43 percent to a median of $27,584.

Less than half of the fines levied between 2001 and 2003 - about $3 million - have been paid.

...

In serious criminal cases, the number of guilty pleas and convictions fell 54.8 percent since 2001. In the first four years of the Bush administration, the federal government has averaged 3.5 criminal convictions a year; in the four years before that the average was 7.75 per year.

And it looks like the reduction in enforcement came from the administration itself:

"Right off the bat, when they [the Bush administration] came in they said we want to focus more on partnerships, alliances, working together with industry," said Celeste Montforton, who was special assistant to the MSHA chief for six years through December 2001. "They did feel there was too much of a focus on enforcement."

Microbiology image library

The American Society for Microbiology has a microbe library that contains lots of resources for educators and students. While many of the materials require a subscription (which I do not have), the site has a free image library that includes such cool things as an animated gram stain, a detailed diagram of the lifecycle of Yersinia pestis, and pictures (and videos!) of a nematode-trapping fungus (so much for all that "fungi are all detritivores" nonsense). All of the images, animations, and videos I've found so far include a detailed summary of what's in the media, making the site very useful.

Making things even better is that the materials are freely available for educational uses, such as:

1) classroom purposes such as faculty presentations and course notes, student presentations and projects; 2) laboratory manuals or handout packets that are assembled by faculty for a single course and disseminated at cost to students enrolled in the course by the faculty or third party vendor such as a campus bookstore; and 3) websites for non-commercial educational purposes. Visual Resources are also available for one time media use without further permission.

Some helpful NSA history

Bruce Schneier has a summary of Project Shamrock, a secret NSA program that collected massive amounts of data on US citizens' communications to and from the United States. The primary difference between Project Shamrock and the NSA program Bush is currently justifying is that Project Shamrock began in the 1950's and collected telegrams, not phone calls or internet communications.

Here's an excerpt from Schneier's post:

A lot of people are trying to say that it's a different world today, and that eavesdropping on a massive scale is not covered under the FISA statute, because it just wasn't possible or anticipated back then. That's a lie. Project Shamrock began in the 1950s, and ran for about twenty years. It too had a massive program to eavesdrop on all international telegram communications, including communications to and from American citizens. It too was to counter a terrorist threat inside the United States. It too was secret, and illegal. It is exactly, by name, the sort of program that the FISA process was supposed to get under control.

(via a post in Pharyngula's comments)

Bush argues for the NSA spying program

The LA Times has a story on Bush's recent attempt to justify the recently revealed NSA spying program:

"If somebody from Al Qaeda is calling you, we'd like to know why," he said. "We're at war with a bunch of coldblooded killers."

...

Bush said Sunday that the program, which the New York Times revealed last month, had been repeatedly vetted by Justice Department officials and members of Congress.

"This program has been reviewed, constantly reviewed, by people throughout my administration. And it still is reviewed," he said.

He also clarified remarks he had made in April 2004, in which he said that all wiretaps required a court order and that "when we're talking about chasing down terrorists, we're talking about getting a court order before we do so."

Asked about those statements Sunday, Bush said: "I was talking about roving wiretaps, I believe, involved in the Patriot Act. This is different from the NSA program. The NSA program is a necessary program."

The president's comments came after he was asked about a newspaper report that a top Justice Department official had questioned the legality of certain aspects of the surveillance, resulting in its temporary suspension. He avoided answering directly and instead raised a spirited defense of the program.

"We're at war, and as commander in chief, I've got to use the resources at my disposal, within the law, to protect the American people," he said.

Rep. Conyers expressed bafflement with the president's statements:

The president tried to assert that the NSA only wiretaps incoming calls without warrants, but the evidence is all to the contrary and Bush's own staff had to explain that he didn't really mean that. This comes on top of yesterday's blockbuster in the Times that the stand up James Comey (who appointed Fitzgerald) had refused to ok the warrantless wiretaps and even AG Ashcroft in the hospital refused to buckle to pressure, for some reason.

And Bob Barr (R-Georgia, 1995-2003) wrote an editorial for Time arguing that the president's NSA program is illegal:

Let's focus briefly on what the President has done here. Exactly like Nixon before him, Bush has ordered the National Security Agency (NSA) to conduct electronic snooping on communications of various people, including U.S. citizens. That action is unequivocally contrary to the express and implied requirements of federal law that such surveillance of U.S. persons inside the U.S. (regardless of whether their communications are going abroad) must be preceded by a court order. General Michael Hayden, a former director of the NSA and now second in command at the new Directorate of National Intelligence, testified to precisely that point at a congressional hearing in April 2000. In response, the President and his defenders have fallen back on the same rationale used by Nixon, saying essentially, "I am the Commander in Chief; I am responsible for the security of this country; the people expect me to do this; and I am going to do it." But the Supreme Court slapped Nixon's hands when he made the same point in 1972. And it slapped Bush's hands when, after 9/11, he asserted authority to indefinitely detain those he unilaterally deemed "enemy combatants"--without any court access.

Bush's advocates also argue that the congressional resolution authorizing military force in Afghanistan and elsewhere--to bring to justice those responsible for the 9/11 attacks--authorized those no-warrant wiretaps. But there is absolutely nothing in the clear language of that resolution or in its legislative history suggesting that it was intended to override specific federal laws governing electronic surveillance. If Bush succeeds in establishing this as a precedent, he will have accomplished a breathtaking expansion of unilateral Executive power that could be easily applied to virtually any other area of domestic activity as long as a link to national security is asserted.

And the NSA story has even motivated Pharyngula to get back into political blogging; he links to supposition that the Bush administration is covering up something much bigger than just wiretapping a few calls from suspected Al Qaeda members.

Crispy mixed rice (gomoku gohan): take 2

One of the great things about gomoku gohan is that it's a very flexible recipe. Our first version seemed a bit vegetable-light, so last weekend we made a vegetable-heavy version.


Gomoku gohan, ready to cook (left) and cooked (right). This has to be one of the prettiest dishes we make.
2 1/2 cups short-grain rice
1 large carrot, peeled and thinly sliced
1/2 small butternut squash, peeled, seeded, and sliced
2/3 cup frozen green beans
2/3 cup frozen corn
6 small red round radishes, thinly sliced
1 chicken thigh (we used a boneless skinless thigh)
3 1/4 cups water (1/4 to 1/2 cup less if your rice is very fresh)
1 packet (0.35 oz) instant dashi powder (or use 3 1/4 cups homemade dashi instead of the water)
1/4 cup sake
3 tablespoons soy sauce
2 tablespoons sugar
1 1/2 teaspoons salt
1 tablespoon vegetable oil

1) In a large bowl, wash the rice and drain it, repeating until the water that drains off is almost clear.
2) Let the rice sit in the bowl, covered with a moist kitchen towel, for one hour. [note: we do not know how essential this step is, but it is apparently traditional for Japanese rice cooking; you might be able to skip it in a pinch.] You can start preparing the other ingredients before the hour is up.
3) If you are making dashi from scratch, prepare it now.
4) If using frozen green beans and corn, defrost them (using the microwave or hot water).
5) Mince the chicken; this is easier if the chicken is somewhat frozen.
6) Add the rice, vegetables, water, dashi powder, soy sauce, sake, sugar, and salt (the chicken and oil will be all that's left) to either a rice cooker or a pot you will use to cook the rice on the stove.
7) Heat the vegetable oil in a frying pan over high heat; once the oil is hot, add the minced chicken and cook until the chicken has lost its raw color.
8) Add the cooked chicken to the rice cooker or pot on the stove, stir to mix (the vegetables may float), and cook the rice. If you have a rice cooker, all this entails is turning the cooker on; for stove-cooking instructions, see my first version of this recipe for instructions.
9) Once the rice has cooked (the rice cooker clicks off), let the rice cooker stay on (on the "stay warm" setting) for another 10 minutes to let the rice brown (the longer you leave the cooker on, the more the rice will brown).
10) Gently mix the rice and serve it hot, being sure to include some of the crispy rice from the bottom in each serving.

Notes:

To compensate for the additional vegetables in this version, we added extra flavorings; we thought the extra amounts worked well. We were out of burdock root when we made this, so we substituted radishes; it seems as though burdock root would have gone well with this mix.

The butternut squash we used was about a pound to begin with; we peeled it with a sharp paring knife. The squash cooked perfectly in the rice cooker; there is no need to pre-cook it.

For more information, see the notes in the original recipe.

Reference:

Yamaoka, Masako. 1984. A First Book of Japanese Cooking: Family-style food for the home. Kodansha International, Tokyo.

Happy New Year!

The decade can't really be half over, can it?