Month: August 2005

Google Desktop 2 — Better, But Still Buggy

Desktop search is one of my obsessions, especially given how much data I tend to generate. Google’s first effort at a desktop search tool left me nonplussed, but the recently released Google Desktop 2 makes quite a few strides in the right direction even if it continues to come up short.

The good news is that Google now includes the ability to index and search a number of additional file types out-of-the-box, including PDFs as well as MP3s and graphics files that have embedded metadata. In addition, it includes a plugin architecture so developers can add the ability for the program to index additional file types.

The program is elegant and simple to use, though it also lacks a lot of the power that the best Windows search product, DTSearch, features. On the other hand, it lacks the unwieldy interface that DTSearch uses to give users access to all that searching power. There’s definitely a tradeoff between the two products in useability vs. complexity of queries.

But the real drawback to Google Desktop 2 from my brief usage is that, like the initial Google Desktop Search product, it chokes on very large file sets which causes regular crashes.

Google Desktop 2 made fairly quick work of my 260,000 archive e-mails, crashing only 3-4 times while indexing them. But when its crawler turned to the My Documents folder on my primary data drive, it was a whole other story. So far, the program has crashed upwards of two dozen times and after almost a week only reached the 46 percent complete marker. Yes, that’s more than 250,000 files so far, but it is very annoying that it cannot index all 160gb worth of PDFs and HTML files without the constant crashing.

It certainly takes DTSearch a very long time to index that huge volume of files, but DTSearch has never crashed on me while indexing. Google Desktop 2 also insists on playing nice and only indexing during “idle time.” The only problem is it never says what triggers “idle time.” I’d prefer to be able to override that setting and have an “index now” button that would just run through the indexing without me having to wonder whether this or that action is going to throttle it back down (for example, even a low-impact task like editing a text file seems to cause Google Desktop 2 to idle).

Probably for most people, the fact that Google Desktop 2 does much of what a product like DTSearch does and at zero cost will render it an ideal desktop search tool. Me, I’m torn between Google Desktop 2 and its elegant interface but crashing problems, vs. DTSearch and its rock-solid performance but uglier-than-sin interface.

Local Paper Screws Up Abortion Story

This sort of story always annoys the hell out of me. The writer here, Emily Walker, had prime front page space for this story about the morning after pill and whether or not it reduces the number of abortions. But instead of helping the reader understand whether or not the morning after pill affects abortion rates, she simply drones on with pointless quotes from different interest groups.

You know its going to be a lousy story when the writer leads off with a statement that is never actually corroborated in the body of the story. So Walker writes,

Southwestern Michigan in 2004 saw its lowest abortion rates in more than a decade, which may be tied to a rapid increase in sales and use of an emergency contraceptive pill and hormonal birth control since 2000.

But there is absolutely no evidence that the abortion rate declined. Rather what declined was the total number of abortions. If the number of abortions declined from 20 per 1,000 to 10 per 1,000, then the rate of abortions has changed. The fact that there were 18 percent fewer abortions in 2004 compared to 1994 just says there are fewer total abortions. But the abortion rate could actually have increased but still result in fewer abortions.

How could that possibly be? Well, one possibility is that there are fewer abortions because there are fewer women of childbearing age in Southwest Michigan. Perhaps women are leaving this part of the state for other parts of the state or even other states. Or perhaps demographic changes such as the increasing aging of the American population or the increasing age at which people get married in the U.S. has also effected Michigan. Don’t worry though, Walker’s article is 100% free of any discussion of demographics that might illuminate a bit better why the total number of abortions declined over a 10 year period.

Something else that might be useful to know is whether or not the birth rate in Southwest Michigan has remained stable or not. If the abortion rate fell, for example, but the birth rate rose, then the hypothesis about the morning after pill would be much weaker. According to the state of Michigan, births are declining overall in Michigan because of the overall aging of the population, which would also tend to reduce the number of abortions. But, that sort of information just couldn’t make it into an article filled with pithy comments such as,

“We attribute it mostly to use of emergency contraceptives,” said Joy Brychta, director of Client Services for Planned Parenthood of South Central Michigan. “As our abortions go down, emergency contraception is skyrocketing.”

I’m sure Ms. Brychta is a nice woman, but what she or Planned Parenthood or Right to Life or the United Nations attribute the drop to is completely irrelevant.

It might also have been helpful to know how abortion rates in other parts of the United States, especially in the Midwest, compare with Michigan’s (assuming we knew what Michigan’s rate was). But all we learn from Walker is,

Michigan as a whole actually saw a four-year upswing in abortions before 2004. Nationwide, numbers have steadily declined in the past two decades.

How big of an upswing? How big of a decline? How about the abortion rate in a nearby state such as Ohio? If the abortion rate has been steadily declining nationwide, is there some demographic trend that Michigan’s finally catching up to? Again, no solid facts, but plenty of nonsense like,

“Those, I suppose, may be factors,” said Right to Life Kalamazoo President Rob Karrer. “But I really do believe that Michigan has been a leader in the country regarding declining abortion rates because of the aggressive nature of the Legislature dealing with the issue.”

Again, I’m sure Mr. Karrer is a nice man, but what he believes might be interesting for a story about whether or not abortion is moral, but it is irrelevant to the issue at hand. And, of course, if Michigan is in the lead in abortion regulation, why that apparent increase from 2000-04?

Source:

Abortions decline; cause debated. Emily Walker, Kalamazoo Gazette, August 22, 2005.
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PETA Suspends Its Slavery Exhibit

It took months before public pressure forced People for the Ethical Treatment of Animals to end its “Holocaust On Your Plate” campaign, but less than a month after the debut of its “Are Animals the New Slaves?” campaign the animal rights group suspended the traveling exhibit.

PETA’s Dawn Carr told the Associated Press,

We’re not continuing right now while we evaluate. We’re reviewing feedback we’ve received — most of it overwhelmingly positive and some of it quite negative.

The NAACP and other civil rights groups vehemently objected to the comparison. NAACP spokesman John White told the Associated Press,

PETA operates by getting publicity any way they can. They’re comparing chickens to black people?

Mark Potok of the Southern Poverty Law Center in Montgomery, Alabama, put it best when he told the Associated Press,

Black people in America have had quite enough of being compared to animals without PETA joining in.

PETA, of course, sees nothing at all amiss about the comparison. According to its web site,

Africans captured and forced into slavery were often compared to animals so as to somehow justify their treatment. They were called “brutes” and “beasts” because of the color of their skin. Their lives were considered expendable, and many died at the hands of their oppressors. The same oppressive mentality behind those actions leads to the slaughter of animals today.

Beatings, lynchings, burnings: These cruel acts happen today just as in the past, only the victims have changed. Cattle and horses are branded with hot irons to mark them as property; elephants used in circuses are captured from their homelands, then beaten with metal “bullhooks” and baseball bats. Cows, chickens, and pigs are strung upside-down before their throats are slit. Many animals are beaten, kicked, and spat upon by farm and slaughterhouse workers who view them as objects of scorn, not as frightened individuals.

Of course the most obvious implication of this nonsense is that African slaves who were being oppressed by the system of slavery were in turn themselves oppressors when it came to the animals they ate. Some slaves, for example, hunted to supplement their meager diet. In PETA’s view, these slaves were no better than those who laid legal claim on them as mere property.

Sources:

PETA suspends controversial exhibit. Dionne Walker, Associated Press, August 17, 2005.

University of Wisconsin Report on Terasawa Research

To: Christine Parks
RARC
From: [REDACTED]
RE: Protocol G00146
Date: July 1, 2003

[REDACTED] and [REDACTED] cross-compared the protocols (see below) and records obtained from all possible sources (e.g., colony records, laboratory note books, check sheets) and compiled a list of discrepancies between approved protocols and actual records. The apparent and potential violations are summarized below. The period of this investigation is from March 2000 to present. The tabulated information in detail is available upon request.

Protocol approval date: 3/13/00 with final amendment on 4/19/00
Major amendment approval date: 10/15/01
Minor amendment date: 05/20/02
Renewal approval date: 04/14/03

1. Apparent Violations

  • Bret left animals during the push-pull-perfusion (PPP) experiment for lunch 4 times. The protocol states that animals will be attended continuously. One animal died in the chair while Bret was at lunch.
  • In 24 PPP experiments in 11 animals, 4 different drug challenges were given. The 3/13/00 protocol did not contain this, but in the 10/15/01 protocol the maximum number of drug challenges was added to be three.
  • Five drugs (the ATP sensitive potassium channel blockers, tolbutamide and glybenclamide; the purinergic receptor blockers, PPADS and suramin; and the ATP hydrolysor, apyrase) that had not been stated in the 10/15/01 protocol were examined with PPP experiments.
  • In 15 PPP experiments ATP doses exceeded the dose range stated in the protocols.
  • In 2 animals more than 12 PPP experiments were conducted (1 animal with 13 times; 1 animal with 15 times). The 3/13/00 protocol did not contain this, but in the 10/15/01 protocol the maximum number of PPP was added to 12.
  • One c-section resulting in a 4th major surgery (the 3/13/00 protocol stated that the maximum number of major surgeries was 3. This confusion occurred because the protocol stated that “the animals used for the project 1 (puberty-project) with PPP experiment can be used for breeding females in project 2, in which 3 c-sections were allowed”.

2. Inadvertent Violations

  • Five animals received reheadcap surgeries. This procedure was not described in the 3/13/00 protocol, but it was added in 10/15/01 protocol.
  • In 15 animals blood draws were conducted on project 2, in which no blood draw was described. In projects 1 and 4 blood drawings are described.
  • In 12 animals more than 4 ml of bloods were drawn in one week. The protocol stated that taking more than 4 ml/week of bloods requires CBC. (See also related problems in No.3).
  • Forty-two animals received higher doses (up to 20 mg/kg) of ketamine. The protocol stated that ketamine dose will be 10-15 mg/kg.
  • Antibiotics were given to 18 animals after PPP experiments. In most cases a staff veterinarian approved the treatment, but consent was not in writing. In fact, Carol Emerson suggested antibiotics after PPP experiments on a regular basis.
  • Prophylactic antibiotics were given before and after surgeries, such as cranial pedestal implantation as well as cranial pedestal repair and removal, in 59 animals. Staff veterinarians knew of this practice, but we failed to describe it in the protocol.

3. Errors due to Reproductive Services for Breeding in Our Animals

  • In 7 animals Reproductive Services took blood samples up to 14 ml in a week under our protocol.
  • Reproductive Services conducted ultrasounds in 8 animals under our protocol. Ultrasound examination was not described in the protocol.

4. Record Errors

  • Fourteen initials/signatures are missing from check sheets.
  • Forty-one hourly check sheets for Chairing/PPP experiments conducted by a former postdoctoral research fellow (Dr. Shinichiro Nakamura) are missing. Since the check sheets had to be displayed on the door of room [REDACTED] when the experiment was conducted, they must have been filled out. However, at this time we cannot locate these records.
  • Errors in computer records are found in the following animals: 
       r94070     6/15/01           Remark by a veterinary assistant says "in chair".
                                However, this animal did not have cranial pedestal at
                                this time and there is no chairing record. So, there is no
                                way that she was in chair.
   r96130     7/10/00-7/14/00   Record says she was in chair after cranial pedestal
                                removal. This is not possible.
   r96112     8/8/00            The animal should be 96119. Record has been corrected.
   r99046     6/12/01           The animal should be 97046. Record has been corrected.
   r98003     6/12/01           The animal should be 98033. Record has been corrected.
   r98040     7/10/01           The animal should be 98049. Record has been corrected.
   r84108     10/3/00           This monkey does not belong to this protocol, because it
                                is a male. To take blood Reproductive Services assigned to
                                our protocol.
   rhaa56     10/3/00           This monkey does not belong to this protocol, because it
                                is a male. To take blood Reproductive Services assigned to
                                our protocol.
   r87100     12/8/00           This monkey does not belong to this protocol, because it
                                is a male. To take blood Reproductive Services assigned
                                to our protocol.
   rhaq36     4/30/01           Cranial pedestal removal surgery was stated as major
                                surgery.
   r93061     3/13/01           Cranial pedestal removal surgery was stated as major
                                surgery.
   rh1935     10/8/01-10/11/01  Chairing is not stated in colony record.
   rh2116     05/14/01          Record states "out of chair on 5/14". But it should be 5/4,
                                because there is no way that she was in chair for 13 days.
   rh2118     04/25/01          PPP experiment was conducted on 4/26/01. The date of
                                the out chair should be 4/26/01.
   r93058     12/10/02          PPP experiment was conducted on 12/11/02. The date of
                                the out of chair should be 12/11/02.
   r96082     11/27/00-11/29/00 Chairing is not stated in colony record.
   r98033     1/6/03-1/8/03     Chairing is not stated in colony record.
   r99031     2/18/02 & 2/19/01 Two records of cannulation. 2/19/01 is correct, based on
                                chairing record.
   r99031     03/12/02          Cannulated three weeks after last time by accident.
                                However no PPP experiment was conducted.
   r99077     09/10/01          Record says that pedestal repair and cannula implantation.
                                Only cranial pedestal repair surgery was conducted.
   r01050     10/14/02          There is no record saying that ketamine was
                                injected.
   rhYO3      05/12/01          Cannulation date should be corrected to 14th, based on
                                the chairing record and the PPP experiment, which was
                                conducted on the 17th.

    5. Others

    • Three animals had skin lesions after chairing.

    * * * * * *

    All “Apparent Violations” were recognized during the review process for the renewal of recent protocol (approved on 04/14/03) and discussed with the Graduate School IACUC. Also, my letter date 6/5/02 in response the Dr. Eric Sandgren’s letter date 5/13/03 dealt with some of the issues. Thus, they have been resolved.

    Most of the “Inadvertent Violations” are due to unrealistic descriptions in the previous protocol or absence of our recognition, e.g., the activity by the Reproductive Services Unit. We will submit an amendment to correct these errors:

    1. A series of 3 ml blood draws up to 12 ml in an experiment will be added to project 2 and project 4.
    2. Ketamine dose will be changed from 10-15 mg/kg to 10-20 mg/kg.
    3. Prophylactic antibiotic treatments before and after surgeries such as cranial pedestal implantation, cranial pedestal repair and removal, will be added to the protocol.
    4. Activities of the Reproductive Services Unit, such as blood draw up to 14 ml/week, ultrasound examination and possible artificial insemination, will be added to the protocol.

    Examination of clinical records from 2000 – 2003 by Christine Parks and Amanda Crumbaugh.

    1. Unsual number of death/serious illness in animals used late 2000 – mid 2002 (23 monkeys used; events of use included even if outside above date range.) Some of the animals were aged. The following are summaries/quotes from the clinical records.
      1. rhap53-Died 6/17/02, 6 days after experiment (push pull perfusion). Necropsy report in clinical record said : “The infarct and thrombus most likely occurred during the experimental procedure 6 days prior to death. They could account for the latered mentation reported clinically, but the ventricular hemorrhage and acute brain swelling are the most probable reason for the monkeys rapid clinical decline and demise.”
      2. rhao21 – In 2001, animal had problems such as lethargy, inappetence, lying down in cage after experiment, cannula implant infection, holding hand stiffly, ulcers. Was noted to have a guarded prognosis but recovered (3/2001). Used again in late 2001 and January 2002; ulcers on 1/29/2002.
      3. 95105 – 3/11 cannulated On 03/15/2002 – poor recovery after experiment (vomiting, lethargy, laying down in cage, dehydrated). 5/28/02 cannula placed. 5/31/2002 – “lethargic and not eating post procedure; evolved to apnea; good hr and pulse; no spontaneous respiration; pc02 61.4 mmttg; pupils fixed and dilated; elected euthanasia – by i.b.” Necropsy: Cerebral/cerebellum edema but no histological diagnosis due to accidental freezing of tissue.
      4. rh2116 – 03/06/2002 – “received emergency (sic) call that chaired animal had died; dead at least 5 minutes (no crt), attempted chest compressions; no heart beat/blood pressure; called pathologist on duty, left message – by [REDACTED]. Three moderate to severe ulcers on caudal thigh, pressure point in chair; blood on ulcers – by [REDACTED] . . .” Blood clot in heart found on necropsy: probably throwing thrombi into circulation. Laboratory notebook noted that something unspecified is “bloody” or “pinkish” while in the chair.
      5. 00046 – 11/08/2002 “in chair on experiment; ulcer (1cm) noted on left foot; cleaned and applied ointment; some swelling of foot, foot is warm; able to use foot and is eating; plan-observe – by [REDACTED]” “removed from cahir (sic) procedure 11-7 p.m.; left ankle appears irritated with open sore present on lateral surface; appears bright, alert, responsive and hydrated with good attitude; discuss treatment with vet- by j.b.”
      6. 00040 – 12/20/200 – “post push-pull observation-animal is lethargic” 12/21/200 – “down in cage; eyes open; will move if touched; push-pull procedure ended 12/20; antibiotic started 12/20; plan- collect cbc/chemistry; monitor closely; [REDACTED] ” Lethargic for a few more days but improved by

    • Primate Freedom Project Publicizes University of Wisconsin Documents on Experiments that Lead to Researcher’s Suspension

    The Primate Freedom Project recently released internal documents it obtained through an open records request about an experiment at the University of Wisconsin that led to a number of primate deaths and, ultimately, the suspension of the researcher.

    Ei Terasawa, a professor or pediatrics at the University of Wisconsin, received approval to do experiments involving primates to study how the animals’ brains developed during menopause.
    But Terasawa’s experiment was plagued by a number of problems. In one case, a monkey died because an attendant left a laboratory for lunch during an experiment. That was just one of at least four times when animals involved in experiments were left unattended when the protocols of the experiment required that someone be present at all times.

    Other monkeys involved in the research were given drugs that had not been approved by the university’s Institutional Animal Care and Use Committee. In other cases, monkeys were given the correct drugs but at dosage levels that had not been approved.

    According to the Associated Press, Terasawa was barred from working with animals for two years and the experiment in question was stopped. Eric Sandgren, chairman of the university’s IACUC, told the Associated Press,

    It’s one of the most severe actions that the committee has ever taken.

    Which seems, frankly, a mild punishment. If dereliction of duty and ignoring experimental protocols that leads to the unnecessary deaths of experimental animals garners only a two year suspension, what would a researcher have to do to be handed a more severe penalty?

    Even more disturbing is that although Terasawa was suspended in 2004, her suspension and the circumstances surrounding it were never made public. The Primate Freedom Project’s distribution of the university’s internal documents on the case were the first opportunity that the public had to learn of this mess.

    Not going public in 2004 about the suspension was beyond stupid. How can researchers expect to be taken seriously when they talk about their commitment to the welfare of the animals they use if they cannot even be open and honest about a case like this? Why in the world did the University of Wisconsin put itself in the position where Rick Bogle was the first person to talk to reporters and the public about the suspension of a research that happened last year?

    The following University of Wisconsin internal documents are available regarding this case:

    Sources:

    U. of Wis. Records Show High Monkey Deaths. Ryan J. Foley, Associated Press, August 16, 2005.

    UW monkey deaths during experiments raise questions. Aaron Nathans, The Capital Times, August 16, 2005.

    Illinois Governor Vetoes Bill That Would Have Legalized Snares

    Illinois Governor Rod Blagojevich recently vetoed Illinois House Bill 1486 which would have legalized the use of snares in wildlife trapping.

    The bill passed overwhelmingly in both the Illinois House of Representatives (87-27) and Senate (49-2). But Balgojevich transmitted the following message of veto,

    August 12, 2005

    To the Honorable Members of the
    Illinois House of Representatives
    94th General Assembly

    Pursuant to Article IV, Section 9(b) of the Illinois Constitution of 1970, I hereby veto
    House Bill 1486, entitled “AN ACT concerning wildlife.” House Bill 1486 allows hunters to use snares to trap animals such as raccoons, foxes and beavers on land. These traps have been banned in Illinois for over 50 years because the trapÂ’s wire hoop strangles the animal. Twenty-one states in the nation do not allow the use of snares.

    Snares are inhumane and indiscriminate. Not only do they cruelly kill wild animals for their fur, they may also kill domestic pets and even endangered species. Even though the bill requires a mechanism on the snare to reduce the chance of strangulation, the safety provisions are still inadequate and animals would suffer unnecessarily. While I support the hunters and trappers of Illinois, I refuse to support this particularly gruesome hunting method thatÂ’s been banned in the state for years.

    For this reason, I hereby veto and return House Bill 1486.

    Sincerely,

    ROD R. BLAGOJEVICH
    Governor

    There is no word yet on whether the House and Senate will try to override the governor’s veto.

    Animal rights groups commended the governor’s veto. In a press release, Camilla Fox of the Animal Protection Institute said,

    We commend Governor Rod Blagojevich for saying ‘No’ to the fur industry’s attempts to further legalize a device that is known to cause immense pain and suffering to animals. With this action, the Governor has made a clear statement that snares have no place in a humane and civilized world.

    The full text of the vetoed legislation can be read here.

    Source:

    Animal advocates commend Governor Blagojevich’s veto of bill that would expand use of cruel snares in Illinois. Press Release, Animal Protection Institute and Illinois Humane, August 16, 2005.