My Political Compass: 2011 edition

The political compass test. My leanings are in line with Gandi, Nelson Mandela, and The Dalai Lama. That seems like respectable company. Interestingly, but not surprisingly, all 2008 candidates for US president, excepting Ralph Nader, Dennis Kucinich, and Mike Gravel, were in the top right corner.

Late Notice for a Presumably Great Radio Show

This morning at 9:00 AM CST Hector Avalos is on the Atheists Talk radio show discussing Biblical Ethics. Hector Avalos is a Professor of Religious Studies at Iowa State University. I expect an enjoyable and thought provoking show.

If you are not in the TCs area you can stream live online. Simply enter a MN zip code, like 55103.

Ill be listening in the car on the journey into the North Country for a couple of weeks.

Groom of Fungus vs. Hymenoptera OR Told you so

Honeycomb

Last Fall I posted on a paper "Iridovirus and microsporidian linked to honey bee colony decline." describing an association between a virus a fungus and the honey bee deaths (colony collapse disorder, CCD) occurring all over the world. At the time I raised several concerns and expressed my skepticism regarding the major conclusions.


One issue that concerned me was that proteins were identified by mass spectroscopy from healthy and sick honey bees. However, only non-honey bee proteins were described. One would expect the vast majority of identified proteins to be honey bee proteins. If we took a skin sample from someone and did mass spectroscopy to see what proteins were there, we would find a ton (figuratively) of human proteins and a pound of microbial proteins from microbes that were living on the piece of skin. A response from Leonard J. Foster highlights how excluding the vast majority of proteins (honey bee), one greatly increases the detection of false positives. This goes a long way to explaining why the most abundant viral proteins were rarely detected. The more a specific kind of protein is in a sample, the stronger the signal you get from the specific protein (actually we are dealing with protein fragments not entire proteins, but the point is the same).


The reason for this is a signal-noise problem. In these types of approaches, you want to remove the strong signals, which overwhelm the data set, to identify the weak signals. The problem is that as we get closer to the limit of detection the difference between a bona fide weak signal and garbage (aka noise) becomes negligible. Think of an eye chart. Your eye is the detector and you want to identify letters. At the top, most people can identify the 'E', which has a strong signal because its so damn big. As you go down the chart it becomes more difficult to identify the letters. With my glasses on I can identify all the letters with 100% accuracy. Without my glasses and from a distance of about 18 inches, I got 1 wrong on line 6 (~83% accuracy), 3 wrong on line 7 (~57% accuracy), and all wrong on line 8 (0% accuracy). So as the signal got weaker, smaller sized letters for my eye detector, my accuracy was less. Importantly, I could see there was something there, but what I interpreted the letter to be was wrong. So, if we asked a population of people to identify these letters, there would be a strong detection of 'E' 'F' and 'P' in lines 1 and 2 and poor detection of 'D' 'O' and 'C' in line 8. The noise comes in because if we ask people, our detectors, to come up with answers on line 8, instead of 'D' 'O' and 'C', we may often get 'P' 'Q' and 'O' respectively. This is our noise. There's something there and we know it, but it is below our ability to accurately figure out what it is. All those Iridovirus sequences identified by Bromenshenk et al may be noise.

Paradise Birdwing, a lepidopteran

A recent paper in PLoS ONE by Tokarz et al, casts further doubt on the link between the virus, at least, and honey bee colony collapse. The virus in question is an Iridovirus family member, which is a poorly studied group of viruses. In this paper, the authors used PCR to detect Iridovirus in a collection of healthy and CCD suffering honey bees. An Iridovirus, IIV24, has previously been associated with disease in honey bees, although not CCD. However, the Bromenshenk paper identified protein sequences most similar to IIV6 and not IIV24. IIV6 infects lepidopteran species, not hymenopterans like honey bees.


So why was IIV6 identified Bromenshenk in the first place? In the October 2010 paper, mass spectroscopy was used to identify proteins. Basically, portions of the amino acid sequence that make up the protein were identified. With these amino acid sequence, we can search protein databases for things that match these sequences. The only genome (DNA) sequence for an Iridovirus that is available is for IIV6. Thus, we can deduce all the protein sequences encoded by this virus. So the amino acid sequences identified by Bromenshenk appear to be most closely related to IIV6 proteins, as opposed to octopus proteins. (see Foster's short rebuttal for why this may likely be an artifact).


To test the idea that IIV6 or an IIV6-like virus is associated with CCD, Tokarz et al tried to detect viral DNA in sick honey bees (and healthy bees, which are predicted to lack the virus if the hypothesis is correct). They made primers that would detect IIV6 directly as well as related viruses based on what we understand to be the most conserved viral proteins. They also made primers to detect IIV24 directly. What did they get? Nothing, Zip, Nada, Zilch. They detected a positive control for honey bee genomic DNA, but obtained nothing for the viral sequences. They also conducted positive controls to show that they could detect viral sequences if it was added to honey bee DNA prior to the PCRs. This sounds like a conclusive result that Iridovirus are not associated with CCD.


However, even though this dataset supports my trepidation of the Bromenshenk conclusions, I am concerned that this study lacks a critical control. I would be much more convinced if the authors were able to detect at least some kind of virus in any of the honey bee samples, even some unrelated endogenous retrovirus. Just something to show they could detect a viral signal from actual samples, not mocked infected samples. The authors did note that it's possible the sick honey bees are infected with an Iridovirus that cannot be amplified with the primers used, which is true.


Finally, I want to hit on an issue you often hear about in the sciences. The myth that 'you cannot publish negative results.' This paper is in fact nothing but a negative result. Yet it is published. Now the authors use other studies to bolster their conclusions, so in fact this work is not simply a negative result. It's a negative result in context. There are many papers that are essentially negative results, although they are cast in a way that is positive. Now you probably won't see papers like this in Science, Nature or Cell, but you also won't find them retracted as often either.


Tokarz R, Firth C, Street C, Cox-Foster DL, & Lipkin WI (2011). Lack of Evidence for an Association between Iridovirus and Colony Collapse Disorder. PloS one, 6 (6) PMID: 21738798

Fungal research does not need death threats

As scientists we have to sell our work. We need to make our ideas as compelling and WOW!!! as possible to obtain funding, get published in the S/N/C glamour journals, and justify ourselves to the greater community and our peers. But we should never jump the shark.


A recent paper from Fungal Biology proceeds to do just that (subscription required). The press glommed onto to this paper with such objective titles as "'My Dishwasher Is Trying to Kill Me': New Research Finds Harmful Fungal Pathogens Living in Dishwasher Seals" and let's not overlook "My dishwasher is trying to kill me! Deadly bacteria found in household appliances" (Really!?! bacteria!?! Really!?!) A reality based article can be found at MinnPost, for which I provided some thoughts.


Now maybe this is the fault of the media, but maybe not. Actually it's not. Well it's both. As far as the media simply reporting what they were told, they are not at fault. As far as the media actually doing their damn job and not simply being a mouthpiece, they are at fault.

The actual title of the paper is "Dishwashers – A man-made ecological niche accommodating human opportunistic fungal pathogens." That seems fairly benign, although the authors are already introducing the "OMG! We're all going to die!!!" meme by focusing on human opportunistic fungal pathogens. (As an aside, I've always been torn by the phrase fungal pathogen. Is it a pathogen that's a fungus or a pathogen of fungi?)

Fungi live here

So the researchers swabbed dishwashers from all over the world, including the US, and found fungi. This is not interesting. Microbes are everywhere. I am not exaggerating, they are everywhere. The freaking original buildings in Antarctica are being destroyed by fungi. What is interesting is that they found certain fungi frequently, suggesting the environmental factors associated with the dishwasher is most favorable to these types of fungi.

E. dermatitidis

The most common fungus obtained was Exophiala  dermatitidis followed closely by Exophiala phaeomuriformis. As expected these yeast grow remarkably well at high temperature (>45°C), high pH (>10 and even up to 12.5), and high salt (17%). These are all conditions, and harsh ones by most accounts, found intermittently in your dishwasher. Personally, I do find this interesting, albeit descriptive. If you check out your dishwasher seals (or even your refrigerator seals), you can often find some dark gunk growing there. In the case of the dishwasher, you have an idea of what the main fungus might be. (I wonder what's growing on the frig, its certainly a different environment from the dishwasher.)


OK, so how is this related to human health, remember the article's title? Well, E.  dermatitidis has been associated with disease in humans, although it is extremely rare. The word 'opportunistic' in the article's title means something. In the case of E. dermatitidis it means there is something wrong with your immune system. Several studies demonstrate that E. dermatitidis colonizes the lungs of Cystic Fibrosis (CF) patients. However, finding something there does not mean that something is causing a problem. Indeed, the very first sentence of the most recent paper on E. dermatitidis and CF reads "The black-pigmented fungus Exophiala dermatitidis is considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients." (emphasis mine) Ooohhh, that's some scary shit.


Hopefully, I've noted how the media went off the rails here. The question now is why? Did they make this hype up? Let's see if the authors of the paper in question have anything to say on the topic. The following quotes are directly from the paper.


"The ability of opportunistic fungi to survive near-boiling temperatures needs special attention." Yeah, yeah, we all think our research needs special attention, but why do these authors think this? Is it because this potentially deadly fungus is coming to get us?


"Roughly one-third of sampled dishwashers was infested mostly with one of the two Exophiala species." Anyone else think the word 'infested' was used primarily to elicit an emotional response?


"The presence of such fungi in dishwashers increases the risk of infection through tableware or otherwise." Well that's pretty damned definitive! Im sure there's a reference with data backing that statement up. What? There's not?!? Well, we all know E. dermatitidis infections have increased markedly since the 1970s when dishwashers became common in US households, wait, we don't know that? How about E. dermatitidis infection rates correlate with number of dshwashers/capita, we don't know that either? Hmm, well are E. dermatitidis infection rates higher in employees how spend their days working with dishwashers than others, we don't know that either? Fine! Let's consider this latter sentence  Fonzi's shark.


You know what jerks my chain the most? This is interesting work. The authors have looked in a previously ignored niche and found some interesting bugs. They provide physiological evidence for why these organisms, and not other organisms, are there. This work provides a way to identify natural niches for E. dermatitidis, look for hot high pH high salt locales. This work also highlights how very little we actually know about the microbial world in which we live. There's no reason to pump up the volume with fear (don't believe there was fear, read the comments following the Daily Mail article).

P. Zalara, M. Novak, G.S. de Hoog, & N. Gunde-Cimerman (2011). Dishwashers – A man-made ecological niche accommodating human opportunistic fungal pathogens Fungal Biology DOI: 10.1016/j.funbio.2011.04.007

A Letter Explaining Science

If you haven't seen this already, you should read it.

Ed Brayton on Atheist Talk

Tomorrow is looking to start off well. Ed Brayton who I know from his Dispatches from the Culture Wars blog is talking with Greg Laden and Mike Haubrich on AM 950 June 12th at 9:00 AM CST. For those outside the Twin Cities you can live stream the station here. (Enter a Minnesota zip code, like 55103)

Ed is a great communicator of the intersection of law science and politics. His blog is such a great read, I can even forgive the fact he is a libertarian. The show should be fun.

Goodbye dear friend

Cupid at Lake Itasca. Age 12.

Yesterday was a hard day, today hasn't been much better. Yesterday I had to say good-bye to an old friend. A friend, a family member, of over fourteen years. It is with great sorrow that I say good-bye to Cupid our dog, companion, quiet supporter after all these years.

It was an otherwise quiet Christmas morning that Cupid entered my life. I was a graduate student in Tucson living with my fiance who has a passion for German Shepherd dogs (all animals actually). Several months earlier we had flown to Reno to breed Viva with a big black gorgeous German Shepherd called Boss, we also used this time as a vacation to see some of Northern Cal including Sacramento, wine country, and San Francisco. That was the time we got through Donner Pass just before it was closed because of the weather.

Viva was now noticeably pregnant and due in the next day or so. She went into labor around 5:00 in the morning Christmas of 1997 and the first pup came shortly thereafter. We had already been through a litter or two and realized this one was not going according to plan. It was taking too long between pups. So shortly after the time most parents are finally rolling out of bed on Christmas, we packed up Viva and, I think, 2 pups and headed to the nearby vet. We spent probably the next 8 - 10 hours celebrating Christmas there with the arrival of an occasional pup, talk about a Christmas present. We weren't at the vet's long before I proposed that if there were 9 pups in the litter, they be named after Santa's reindeer. The general approach was to use a letter of the alphabet and name all the puppies using that letter. But it was Christmas! This suggestion was approved and needless to say Blitzen, Comet, Cupid, Donner (I know), Vixen, Dasher, Dancer, Prancer, and Rudolph (the one nut wonder) arrived throughout the day. I could tell you stories about Blitzen and Vixen as puppies and young adults, but Cupid was the one who stayed in the family and stays in our hearts.

When Cupid was a young adult, I moved away to start a post-doc in New York. Because we had some dominant personality and older German Shepherds, Im looking at you Fia and Dancer (different litter), Cupid seemed kind of hidden in the background. When I was home, she didn't run around screaming 'look at me! look at me! see what I can do!' like the others. In the pack hierarchy she was low girl on the totem pole, but she didn't cower or hide. She just blended. Maybe this has more to do with the little time I got to spend with the dogs during this time because I was only back every few months.

I lived apart from my family for a couple of years and then landed a position in Minnesota. I moved my stuff there from New York and headed to Arizona to get the family. We had lost the other dogs and only had Cupid left to make the trip with us. So, a moving truck loaded up the household items and furniture  and we took Cupid in the minivan with us. Cupid got to see Northern Arizona (again), Utah, Wyoming, South Dakota (where she visited Mt. Rushmore and saw the 'wild' donkeys), and finally Minnesota. All this and only 4 years old.

We rented a townhome for the first year we were in the Twin Cities area out in the boonies. Cupid spent her days hanging out there, but got long walks in the wooded areas around us each morning and afternoon. There were some commercial-industrial places that had large grassy areas and ponds, not to mention Otter Lake, nearby wildlife center, and the wetland area right next door. During the winter, we often walked on 'Squirrel Trail' which was a short nearby trail that surprisingly enough housed many squirrels. There were geese in abundance most of the year, and goslings some of the year. There were also deer more often than not. We almost lost Cupid early on when she decided to chase a flock of geese that flew over the road near the townhomes. We also had turtles running, well not running, around. One afternoon a turtle was scratching at our sliding door, I guess it was too lazy to go around the townhomes and wanted to cut through our place. Anyway my now wife opened the door so Cupid could say hi. I saw the turtle and shouted "Get Cupid back from" and didn't bother finishing because Cupid had just yelped and jumped back about 10 feet with a gash on her nose from the snapping turtle she was checking out. She kept a small scar on her nose from that encounter.

Cupid moved into the house we bought later that year and truly enjoyed having a private grassy backyard and deck to take sunbaths in. She also enjoyed her new job of keeping rabbits and squirrels on their best behavior as well as making sure the neighborhood cats, whose owners cant bother to take care of them, do not spend any amount of time in the yard hunting birds. This explains why the cardinals and blue jays always seemed to appreciate her.

At this point Cupid entered he professional career. She tried her paw as a sheepherder but decided early on that if she couldn't actually catch them, what was the point. She then moved over to tracking and showed some real potential. I remember one time we had traveled to Wisconsin with the tracking club and my wife, 7 or 8 months pregnant at the time, had just finished a long track that Cupid did awesome at. As they were walking back across this large field that was filled with all these divots, my wife disappeared into the grass, bounced right back into view saying "Im alright," and instantaneously disappeared into the next divot with the timing perfect for a prime time comedy. (Neither mother nor child, AFAIK, were harmed in the two crashes.) When they got back to us, Cupid was quite proud of her accomplishment on the tracking course, although I think I detected some ridicule at all us two legged mammals that have intrinsic issues with gravity.

Cupid was 6 when our son was finally born. The first night after he was delivered, I went home to take care of her and brought a blanket my son had been swaddled in for her to get used to his scent. I honestly had some trepidation about how the new arrival would go over. However, Cupid had no problems acclimating to him. She was the perfect grandmother. I would say mother, but anyone who has had a litter knows the moms are perfectly happy to bite, albeit gently, the puppies little heads when they get annoying. She often slept next to his crib and always checked his baby swing in the morning which was where he often slept.

Things pretty much settled down after that. There were frequent walks in the wooded area next to our house. (Its somewhat ironic that that area is being ripped up and replaced with houses starting this summer.) There were also many walks to the nearby lake with swimming and around the wetland across the street. She took on the habit of waiting until you were doing dishes or looking for something in the refrigerator and then stopping right behind you to see if she could trip you (Im pretty sure that was her way of rubbing in our faces that two-legged animals are more easily toppled).

I think Cupid was 8 when we learned she had degenerative neuromyopathy. This is a neuromuscular disease that seems to affect German Shepherds more than other large breed dogs. It causes the slow loss in muscle tone and function. With age comes interesting new growths, loss of hearing, and eyesight problems. This is also true in dogs. But the old girl got around just fine. She had to stop going up and down the basement stairs and for awhile I carried her up and down them so she could hang out with Alpha. As time went on, we started covering the wood floors with carpets because her back legs would slip too easily. Finally, last summer I built a ramp from the deck to the lawn so she didn't have to even use those steps.

During all this time she was basically happy and enjoyed being with the family, going for rides in the car, sun baths. But this last week she finally started having leg pain that we couldn't remedy. This had become a more recent problem, but would generally clear up after a nights rest. This time was different. I could see it in her eyes that this wasn't resolving, that it wasn't fun anymore, that the time had come. The vet was great and Cupid got to stay in the car for her final goodnight, she never was a fan of a Vet's office.

I do not believe in heaven or the afterlife like most people do when they say these terms. But Cupid was an important part of my life for over 14 years. Because of her I am not the same person I would have been if I didn't have Cupid. So I can honestly say that Cupid lives on in me. I can also say that in a way, since  I affect others, Cupid is playing a part in those interactions and maybe that's what the afterlife is or at least that's all it needs to be to me. So as tears wet my cheeks again I just want to say goodbye dear friend, I miss you.

Cupid: 12/25/1997 - 6/8/2011