May 2004 Archives

Tangled Bank

I’m hosting the forth tangled bank in two days. Please send in your entries if ya got them.

Panda’s Thumb Posts

Blog For Democracy

I’ve added a new blog to my list: Blog for Democracy. It is run by a group of progressives in my lovely home state: Georgia for Democracy. As you can probably guess, they are former Howard Dean supporters.

The US government said it would ban homosexuals from making anonymous donations to sperm banks, in the name of preventing transmittable diseases, in a move swiftly condemned by gay rights groups.

New Food and Drug Administration rules that take effect May 25 require agencies that collect tissues or cells including sperm to ask the donor if he has had sex with men or used injectable drugs in the past five years. If the answer is affirmative in either case no donation is allowed.

This is total bullshit. It sounds like a bunch of homophobia to me. Heck it might even be eugenics if we all didn’t know that homosexuality was obviously a choice. ‘Cause I know I remember making a choice between innies and outies.

I went to the FDA website and found their guidelines for tissue donation. You can look at it to see what the requirements are; they begin on page 16. The top one on the list is not having hot gay sex in the last five years. (I’m gonna get a Google hit from that one.)

I also found a transcript from an FDA conference where the issue was discussed.

The following was very enlightening. It begins on page 160.

[MR. TREEIMAN:] Now, in 1981, 20 years ago, I started a group for lesbians and gay men to have children together, and in 1982, I was one of the foremost loud mouths in my community to stop lesbians and gay men having children together because of the dangers of HIV. I was doing the FDA’s job 20 years ago.

If the FDA had come up with this proposal in 1985, I would be supporting it. I would have supported it back then. But with what we know now about the window period and HIV testing and its efficacy and the quarantine period, these are not appropriate for the year 2002. …

Now, some in the FDA has taken the Young Gay Men Health Study and extrapolated that inappropriately to all gay men. And I fail to see how the sexual habits and the HIV prevalence rate of men in their early 20s who are, for the most part, recruited from sexual venues relates to men in their 30s and 40s who are in long term mutually monogamous relationships. In fact, to take that number defies any sort of scientific mind set or dignity. One has to suspect that in order to snatch at that number, there are other reasons for it.

The first time I heard of that was at the CDC conference last year, and someone from the FDA did appropriately expropriate the Young Gay Men’s Health Study number to all gay men in general, and I said that’s an inappropriate thing to do. And he said to me, “Do you have a better number I can use?” His unscientific method seizing upon this number, regardless of how inappropriately, left me in stunned silence. But, sir, I say to you today I do have a better number, and it matches Dr. Dayton’s number of zero. I simply studied the men who presented at my sperm bank. If we’re going to talk about men, gay men, MSMs who might potentially be donors, let’s look at them at the only sperm bank. And you have in your possession my study, 72 men screened as I have said, but in addition to that in addition to that, we asked them very detailed questions about their sexual behaviors. And we came up with criteria that identity release donors because I only work with identity release donors, which are the same, once again, in terms of safety as anonymous donors, is that they had a previous negative HIV test and had not had a sexually transmitted disease during the last five years and had never had syphilis or were celibate or in a long term mutually monogamous relationship with a cohabitating HIV negative partner or were single and did not engage in rectal sex or engaged in rectal sex but only used condoms without breakage you have to ask very specific questions and did not engage in oral sex or engaged in oral sex without ejaculation in the mouth.

Now, oral sex is a big bugaboo. A lot of people say that it’s a safe practice. It is not a safe practice. It is a very low risk practice, but it is not a safe practice, and it is around the issue of oral sex and I’m really amazed that we haven’t been talking about more about oral sex and directed donors here this morning. It is around the issue of oral sex that we need to ask people, Are you engaging in unprotected oral sex with partners you don’t know their sero status or partners who you know to be positive?

The result of my study is that all 72 men came up negative. …

I bet if I did a study on heterosexual men who participated in risky sex and extrapolated it to all heterosexuals, I could eliminate even more potential sperm donors.

Tangled Bank #3

The third installment of the Tangled Bank is up at 10000 birds.

I get to host it in two weeks.

References

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I was board this morning, so I decided to examine my access logs. Using a perl script that I whipped up, I have produce a table of the domains that send things my way. The Panda’s Thumb and Pharyngula are at the top of the list. There are also various flavors of Google in the list. I decided to leave the spam in the list because I’m lazy.

DomainTimesDomainTimes
pandasthumb.org670 pharyngula.org604
laero.cyberdot.nl118 google.com111
bloglines.com108 ministeriovidaa.com.br84
evolutionblog.blogspot.com68 mblog.com60
smijer.com48 216.239.39.10445
iidb.org40 216.239.51.10439
search.yahoo.com37 darwin.bc.asu.edu36
home.rochester.rr.com35 pharyngula.com30
kenethmiles.blogspot.com23 tangledbank.net23
sitemeter.com18 technorati.com14
216.239.37.10414 strangedoctrines.typepad.com11
google.it10 216.239.57.10410
decorabilia.blogspot.com10 bisso.com9
livejournal.com9 toolbar.google.com9
google.co.uk8 cotch.net8
google.de8 blo.gs8
aeternam626.com7 wam.umd.edu7
google.ca6 amateurxpass.com6
xuande.livejournal.com5 translate.google.com5
129.219.245.625 gallerylisting.com5
64.233.167.1045 google.fr4
google.com.au4 google.co.in4
216.239.59.1044 hallofmaat.com4
search.netscape.com3 evowiki.org3
wiki.cotch.net3 paris-hilton-video.blogspot.com3
us.f114.mail.yahoo.com3 nudecelebblogs.com3
geocities.com3 shatteredreality.net3
us.f612.mail.yahoo.com3 mysearch.myway.com2
answerbus.com2 natcenscied.org2
p082.ezboard.com2 metamirror.org2
google.es2 steinsky.me.uk2
google.fi2 evcforum.net2
english.spampoison.com2 freenudecelebrity.net2
google.nl2 google.ch2
sciteacher.com2 scienceport.org2
br.cade.busca.yahoo.com2 kinja.com2
aolsearch.aol.com1 msxml.excite.com1
SpamPoison.com1 google.co.ve1
external.paltalk.com1 google.com.br1
google.be1 radiovoxpopuli.org1
google.com.sg1 thehallofmaat.com1
google.co.il1 google.pl1
google.co.hu1 blogshares.com1
baidu.com1 google.co.nz1
freewebcams.reallyconfused.com1 websearch.cnn.com1
google.com.gr1 ref.spoof.org1
stcynic.blogspot.com1 google.ie1
groups.yahoo.com1 1142.net1
google.com.ar1 dogpile.com1
home.bellsouth.net1 physicsforums.com1
search.virgilio.it1 blogger.com1
google.com.1 google.se1
pi-o.com1 britneyspearsnude.blogspot.com1

Borneo Chela

I’ve added a new biology blog to my links: Borneo Chela. It’s run by a doctoral student at UMD.

Check out the cool posts on Cicadas.

Whence the giant panda?

Well the Panda’s Thumb’s first poll is over and the majority of the five hundred and nine votes cast say that giant pandas are not bears: 28% yes, 62% no, and 10% dunno. I hate to say it, but the majority is wrong.

Giant pandas (Ailuropoda melanoleuca) form the most basal branch of the bear family. The figure below shows the relationship of the bears to the rest of the extant order Carnivoria (Mammalia). It is the composite of two maximum parsimony phylogenies, Figures 1 and 8 of Bininda-Emonds et al. (1999), derived from data present in scientific literature. The scale of the tree is millions of years before present and was derived from data in Tables 2 and 9 of Bininda-Emonds et al. (1999).

The giant panda first appears in the fossil record about 3 million years ago during the Early Pleistocene. It had a wide distribution in the Pleistocene ranging from Myanmar to eastern China and as far north as Beijing (Schaller et al. 1985 p11 ). The giant panda lineage branched off from the other bears around 22 million years ago (Bininda-Emonds et al. 1999). It has been suggested that the giant panda is a descendent of Agriarctos, a “small, bearlike animal of the Ursavus lineage from the mid-Miocene in Europe” and the last surviving member of Ursidae subfamily, Agriotherinnae (Schaller et al. 1985 p229).

Although, there used to be a debate on whether the giant panda was more closely related to raccoons or to bears, multiple studies since the 1960s established its connection to the other bears. In 1869 the giant panda was first discovered by western zoologists and described as a new species of Ursus. However, the next year another zoologist claimed that the giant panda was not a bear but a relative of the red panda, which was at that time believed to be related to raccoons. In 1964, D. D. Davis published a comprehensive, comparative anatomical study that showed that the giant panda was a bear adapted for a particular food niche. After that, only a few zoologists held on to the idea that they two pandas were close relatives (Mayr 1986). Molecular studies beginning in the mid 1980s helped support the conclusion of anatomists and paleontologists.

O’Brien et al. (1985) used DNA-DNA hybridization, isozyme genetic distance, immunological distance, and karyotype evidence to estimate the relationships among the giant panda, red panda, and their supposed closest relatives. They concluded that the giant panda’s closest relative were the other bears.

Molecular and cytological methods specify the divergence of the giant panda from the ursid lineage of the carnivores at 15-25 Myr BP, whereas ancestors of the [red] panda emerge very near the time of the procyonid-ursid split.

(O’Brien et al. 1985)

Wayne et al. (1989) used similar methods to study a larger picture of carnivore evolution and similiarly concluding that the giant panda was a basal lineage of the bears.

The consensus treee indicates that between 30 and 40 M.Y.B.P. the progenitor of modern ussids and procyonids split into two lineages. Within 10 million years of that event the procyonid group split into Old World procyondis represented today by the red panda and the New World procyonids (for example, raccoons, coatis, olingos, kinkajous). Approximately 18-25 M.Y.B.P. the ancestor of the giant panda … diverged from the ursid line. The next divergence is between teh ursine bears and the spectacled bear … which occured between 12-15 M.Y.B.P. The lineages leading to the remaining species–the brown bear … the black bear … the sun bear … and the sloth bear … –first became distinct 5-7 M.Y.B.P.

(Wayne et al. 1989)

Goldman et al. (1989) used one- and two-dimensional protein electrophoresis to estimate the molecular distance among the eight species of bears, raccoon, and red panda.

The addition of two new data sets relating 289 proteins resolved by 2-D gels and 44 allozyme systems from living ursid species plus two procyonid species provides a corroborative basis for interpreting the evolutionary history of this group. The results were in topological agreement with each other and with previous phonetic trees derived using DNA hybridization, albumin immunological distance, and allozyme genetic distance (Sarich, 1973; O’Brien et al., 1985). The cumulative data suggestions an ancient ologocene split of the ursid and procyonid progenitors. Within then million years of that event, the red panda diverged from the lineage that lead to the raccoon. Modern procyonids consist of 19 distanct species, and all but the red panda are found in the New World (Nowak and Paradiso, 1983).

Within the ursid radiation, there are three primary divergence nodes that consistently appear. The earliest is the line that lead to the giant panda, the second lead to the spectacled bear, and the third is a polytypic divergence node with lead to the speciation of size species of usine bears. The divergence relationship among ursine bears was not resolved with any of the molecular data sets with the exception of the affirmation of the close affinity of the brown bear and the polar bear.

(Goldman et al. 1989)

Hashimoto et al. (1993) studied alpha- and beta-hemoglobin sequences from various carnivores using maximum likelihood. They also concluded that the giant panda’s closest relatives were the other bears.

And finally, in a recent study using DNA fingerprinting, Wan et al. (2003) conclude that the giant panda may have two subspecies, Quiling and Sichuan.

Based on the large genetic difference between the QLI [Quiling] and Sichuan populations, we hypothesized that the giant panda may have differentiated into two subspecies. Key morphometric measurements were taken from 37 adult skulls . … The results revealed very significant differences between the QLI and Sichuan populations, with 7 morphological parameters. The measurements indicate QLI giant pandas had smaller skulls than Sichuan individuals. The molecular and morphological evidence indicates that two subspecies of the giant panda have formed . …

(Wan et al. 2003)

References

References

  • Bininda-Emonds ORP, Gittleman JL, and Purvis A (1999) Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74 pp143-175
  • Goldman D, Giri PR, and O’Brien SJ (1989) Molecular genetic-distance estimates among the Ursidae as indicated by one- and two-dimensional protein electrophoresis. Evolution 43(2) pp282-295
  • Hashimoto T, Otaka E, Adachi J, Muzuta K, and Hasegawa M (1993) The giant panda is close to a bear, judge by α- and β-hemoglobin sequences. Journal of Molecular Evolution 36:282-289
  • Mayr E (1986) Uncertainty in science: is the giant panda a bear or a raccoon? Nature 323 pp769-771
  • O’Brien SJ, Nash WG, Wildt DE, Bush ME, and Benveniste RE (1985) A molecular solution to the riddle of the giant panda’s phylogeny. Nature 317 pp140-144
  • Schaller GB, Jinchu H, Wenshi P, and Jing Z (1985) The Giant Pandas of Wolong. The University of Chicago Press.
  • Wan QH, Fang SG, Wu H, and Fujihara T (2003) Genetic differentiation and subspecies development of the giant panda as revealed by DNA fingerprinting. Electrophoresis 24 pp1353-1259
  • Wayne RK, Benveniste RE, Janczewski DN, and O’Brien SJ (1989) Molecular and biochemical evolution of the Carnivora. in Carnivore Behavior, Ecology, and Evolution. ed. Gittleman JL. Cornell University Press

Note: originally posted here.

Abu Ghraib Report

You can download the report of the military’s investigation into the torture of prisoners in Abu Ghraib to obtain information.

6. (S) I find that the intentional abuse of detainees by military police personnel included the following acts:

  • (S) Punching, slapping, and kicking detainees; jumping on their naked feet;
  • (S) Videotaping and photographing naked male and female detainees;
  • (S) Forcibly arranging detainees in various sexually explicit positions for photographing;
  • (S) Forcing detainees to remove their clothing and keeping them naked for several days at a time;
  • (S) Forcing naked male detainees to wear women’s underwear;
  • (S) Forcing groups of male detainees to masturbate themselves while being photographed and videotaped;
  • (S) Arranging naked male detainees in a pile and then jumping on them;
  • (S) Positioning a naked detainee on a MRE Box, with a sandbag on his head, and attaching wires to his fingers, toes, and penis to simulate electric torture;
  • (S) Writing “I am a Rapest” (sic) on the leg of a detainee alleged to have forcibly raped a 15-year old fellow detainee, and then photographing him naked;
  • (S) Placing a dog chain or strap around a naked detainee’s neck and having a female Soldier pose for a picture;
  • (S) A male MP guard having sex with a female detainee;
  • (S) Using military working dogs (without muzzles) to intimidate and frighten detainees, and in at least one case biting and severely injuring a detainee;
  • (S) Taking photographs of dead Iraqi detainees.

8. (U) In addition, several detainees also described the following acts of abuse, which under the circumstances, I find credible based on the clarity of their statements and supporting evidence provided by other witnesses (ANNEX 26):

  • (U) Breaking chemical lights and pouring the phosphoric liquid on detainees;
  • (U) Threatening detainees with a charged 9mm pistol;
  • (U) Pouring cold water on naked detainees;
  • (U) Beating detainees with a broom handle and a chair;
  • (U) Threatening male detainees with rape;
  • (U) Allowing a military police guard to stitch the wound of a detainee who was injured after being slammed against the wall in his cell;
  • (U) Sodomizing a detainee with a chemical light and perhaps a broom stick.
  • (U) Using military working dogs to frighten and intimidate detainees with threats of attack, and in one instance actually biting a detainee.

Mission not accomplished

A terrorist cell which has moved into Iraq since we destabalized the region has beheaded an American citizen in revenge for the torture of Iraqis in Abu Ghraib prison.

We encourage them; they encourage us; and the cycle continues.

Iraq is a fucking war zone. Mission not accomplished. Our adminstration needs to suck up their hubris and bring the civilians home.

Torture

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The following letter appeared in my local paper today.

“Publicity of Iraqi prisoner abuse rooted in liberal media bias”

I’m sorry that must not have been good journalism, or maybe it just didn’t have the anti-Bush, anti-American theme the “media” seem to thrive on these days. I for one think the “media” should concentrate more on unbiased reporting and not so much on pushing their liberal agenda. You have to remember, you do have conservative readers, and we would like something to read too.

Eric Bryant

Madison

There is just so much wrong with this. The fact that this man believes that, as a conservative, he shouldn’t have to read stories about torture in American-run prisons in Iraq scares me. Clinton getting a blow job was a scandal; this is a disaster.

These Iraqis were tortured by military intelligence for information. They did not disserve it; no one disserves it. It was a failure in the chain of command to allow this to occur. To put people in charge of a prison without adequate training is irresponsible. Maybe because many of the reservists were prison guards back in the States they thought they had enough training already. Of course, how much training does it take to say “don’t fuckin’ torture people.” My mother could have done that.

These were war crimes. These were crimes against humanity. The Bush administration and the chain of command should not get a pass on this. The American people need to stand up in November and say “enough.”

School’s Out

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Well I just finished my last class exam of my educational carreer. Now just need to finish up the projects I’ve worked on, write them up, and I’ll be good to defend.

Back to the grind … after some sleep.

Schaefer Remix

An updated version of my piece on Dr. Fritz Schaefer is available on the Panda’s Thumb.

Religiously Motivated Incredulity

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