31st meeting of the skeptics circle

Abel Pharmboy at Terra Sigillata has hosted one of the biggest skeptics circles I've seen in a while. There is a plethora of skeptical entries this week on a wide range of topics so it's well worth the visit. The next circle is being hosted by our very own pooflinger at Pooflingers Anonymous so presumably check over there for contact details.

What evidence suggests badgers infect cattle with M. bovis?

Part III: Mycobacterium bovis, the English bovine tuberculosis outbreak, badgers and the culling debate.

Critical to the entire culling controversy as a control measure for M. bovis is what the exact role of the Eurasian badger (Meles meles) in the spread of bovine tuberculosis. If badgers are the principal source of bovine tuberculosis, then a cull would make sense and would have the maximum effect on reducing breakdowns (a case of bovine tuberculosis in a cattle herd). If badgers are not the principal source of bovine tuberculosis, or alternatively they are but cannot spread bovine tuberculosis to cattle, then a cull is just going to be a needless waste of time with ultimately no effect as several conservationists have argued. So what does the scientific literature actually say?

Are badgers actually infected with bovine tuberculosis and if so, can they secrete Mycobacterium bovis?

One of the most recent studies relevant to this question is from Chambers et al., (2002) and investigated the current serological tests for identifying badgers that shed Mycobacterium bovis. This study compared two methods, notably ELISA (Enzyme Linked ImmunoSorbent Assay) and Western blotting against direct culture of M. bovis for accurately identifying infected badgers. Importantly, this study was set up to determine if these techniques could accurately determine if a badger was secreting M. bovis. Essentially, the scientists picked an area that had endemic infection with M. bovis among cattle herds and captured 128 badgers. Of these sampled badgers, 44 were confirmed to have secreted M. bovis at some point in their life as confirmed by the ELISA, Western blot and culture detection methods.

With the use of all three methods concordantly it makes it virtually impossible that the result is incorrect or outside factors such as other environmental mycobacteria (Primm et al., 2004) are responsible and as such, the study clearly implicates badgers as a host for M. bovis. Of course, science does not stand simply by itself but rather through the work that others have done in the past and what studies have followed afterwards. Here the consensus is overwhelming. For instance, a previous study from Gallagher and Clifton Hadley (2000) shows that badgers had M. bovis infection in both lung tissue and in their urine from post-mortem examination. Other studies from Costello et al., (1999) and Olea-Popelka et al., (2005) have found that badgers are infected with M. bovis and most importantly, the same strains of M. bovis tend to be shared between cattle and badgers in the same area (this is an important point, more on this later however).

Further, the two key ‘trials’ conducted on the effects of badger culling by Donnelly et al., (2002, 2006) in England and the “Four counties” trial in Ireland by Griffin et al., (2005). Both of these studies have found that bovine tuberculosis is present among badgers around farming areas. Typical prevalence of infected badgers tends to fluctuate widely, with some researchers finding infection rates around 20% and others up to 50% (Corner L.A.L., 2006). In short, numerous studies have all universally been able to find badgers that have been infected with M. bovis. The question remains as to if infected badgers secrete M. bovis that can infect cattle?

In order to spread efficiently from badgers to cattle it’s important to realize that several factors need to occur for any chance of transmission:

1) Badgers need to come into contact with cattle or alternatively, cattle come into contact with feces and other excretions of badgers.

2) Infected badgers must be able to secrete M. bovis to cattle through excretions such as sputum and urine.

3) M. bovis in badger excretions must have some mechanism to survive the passage from a badger to cattle.

We should also expect if these three things are found and that if badgers are transmitting M. bovis to cattle (somehow), then we’d also expect to see the same spoligotypes in cattle and local badgers. So once again, what does the literature say on these three issues?

Possible means of transmission of cattle to badgers.

Several studies have identified that badgers are not afraid to come into contact with cattle, although the circumstances in which badgers come into contact differ. Phillips et al., (2003) and Corner L.A.L. (2006), both report that cattle will typically avoid badgers if at all possible. Interestingly, both papers note that heavily infected badgers tend to behave aberrantly and that cattle will frequently investigate by licking, sniffing and biting. This matches similar observations of cattle in New Zealand investigating brushtail possums that are dying of TB.

Additionally cattle are also highly likely to come into contact with the excretions of badgers such as urine, feces and sputum. As badgers excrete copious amounts of infectious bacteria in their sputum (coughed up fluid), urine and from infected bite wounds this does pose a possible risk for cattle grazing in fields visited by badgers (Krebs et al., 1998; Phillips et al., 2003; Scantlebury et al., 2004 and Young et al., 2005). Additionally, badgers are also capable of surviving with tuberculosis for months or even years and may be infectious for long periods of time, until they eventually succumb to infection (Phillips et al., 2003; Scantlebury et al., 2004 and Corner L.A.L., 2006).

Finally, it is also the case that cattle will graze areas that have been used as latrines or ‘crossing points’, essentially places badgers tend to go over often when moving from field to field, which poses a potential risk of ingesting M. bovis. Interestingly the main means of infection in cattle is from aerosolized particles and not from ingestion. This is supported by the fact infected lesions and bacteria from infected cattle are typically isolated from around the head region more so than GALT* (Phillips et al., 2003).

Scantlebury et al., (2004) noted that intensively farmed cattle tended to graze badger latrines and crossing points immediately due to sward (grass) competition. Conversely, cattle farmed in less dense numbers tended to scratch and sniff latrines or badger urine (crossing points) but ultimately avoid these areas. Rates and reasons for cattle investigation or consummation of swards infected with badger excretions should deserve further analysis.

Finally M. bovis is more than capable of surviving outside of the host once it has been excreted. As mentioned in part II, mycobacteria are particularly hardy organisms and have a wide metabolism. M. bovis in soil samples has been demonstrated to be viable for months by culture and may even be viable for years (Young et al., 2005). This is because although previous studies that have failed to culture M. bovis after long periods of time, molecular methods for the detection of RNA have indicated the organism could still be present but non-culturable (Young et al., 2005). In a similar manner to other microbes, it is possible for a viable organism to exist in the environment that cannot be cultured for whatever reason (Colwell and Grimes, 2000).

The final link in the chain.

Generally infected badgers tend to be found in clusters, with the surrounding cattle farms also infected with the same strains of M. bovis (Costello et al., 1999; Smith et al., 2003; Griffin et al., 2005 and Olea-Popelka et al., 2005, 2006). Additionally, many studies have indicated that badgers may roam relatively widely and have varying levels of contact with cattle, see for examples Griffin et al., 2005 and Olea-Popelka et al., 2006. As mentioned earlier, this concordance between the general spoligotypes in an area being the same between those found in infected cattle and nearby infected badger setts resolves the issue. It’s almost certain that badgers are to some degree responsible for spreading M. bovis to cattle, even if the exact mechanism is unknown and has yet to be illucidated (Olea-Popelka et al., 2006).

It’s very clear that badgers can be infected by M. bovis, excrete the organism in their sputum and urine due to chronic infection of the lungs and kidneys and that the same strains of M. bovis that infect badgers are found in cattle. Also importantly, the proactive culling portions of the Donnelly et al., (2003, 2006) study and the Griffin et al., (2005) “four counties” trial have shown considerable drops in the prevalence of herd breakdowns**. Finally however, if you’re the sort of person who requires a more ‘visual’ aid, then I would propose having a look at this poor badger (Horrific image! Do NOT click it unless you like copious amounts of pus!), which has died of tuberculosis and believe me, it’s not a pretty sight.

However, despite the strength of the evidence presented from the literature supporting a link between badgers and bovine tuberculosis, it’s insufficient to resolve the issue mentioned in the opening paragraph. Even if badgers are responsible for spreading tuberculosis, the role of cattle will also need to be determined as it may be possible that badgers are only a symptom, and not the cause of the high prevalence of BTB in the UK. Keep checking back soon for this question to be addressed in Part IV: The role of cattle movements in the bovine TB epidemic.

*GALT=Gastrointestinal Associated Lymphoid Tissue.

**I will point out before someone else does, that I’m aware the reactive culling part of the Donnelly studies have shown an increase in herd breakdowns. I’m not deliberately ignoring this point as I intend to cover this later in the series.

References

Chambers M.A., W.A. Pressling, C.L. Cheeseman, R.S. Clifton-Hadley and R.G. Hewinson (2002). Value of existing serological tests for identifying badgers that shed Mycobacterium bovis. Veterinary Microbiology, 86:183-189.

Colwell R.R. and Grimes D.J. (2000). Nonculturable microorganisms in the environment. ASM press Washington D.C.

Corner L.A.L. (2006). The role of wild animal populations in the epidemiology of tuberculosis in domestic animals: How to assess the risk. Veterinary microbiology, 112:303-312.

Costello E., D. O’Grady, O. Flynn, R. O’Brien, M. Rogers, F. Quigly, J. Egan and J. Griffin (1999). Study of restriction fragment length polymorphism analysis and spoliogotyping for epidemiological investigation of Mycobacterium bovis infection. The Journal of Clinical Microbiology, 37:3217-3222.

Donnelly C.A., R. Woodroffe, D.R. Cox, J. Bourne, G. Gettinby, A.M. Le Fevre, J.P. McInerney and W.I. Morrison (2003). Impact of localized badger culling on tuberculosis incidence in British cattle. Nature, 426:834-837.

Donnelly C.A., R. Woodroffe, D.R. Cox, F.J. Bourne, C.L. Cheeseman, R.S. Clifton-Hadley, G. Wei, G. Gettinby, P. Gilks, H. Jenkins, W.T. Johnston, A.M. Le Fevre, J.P. McInerney and W.I. Morrison (2006). Positive and negative effects of widespread badger culling on tuberculosis in cattle. Nature, 439:843-846.

Gallagher J. and R.S. Clifton Hadley (2000). Tuberculosis in badgers: a review of the disease and its significance for other animals. Research in Veterinary Science, 69:203-207.

Griffin J.M., D.H. Williams, G.E. Kelly, T.A. Clegg, I. O’Boyle, J.D. Collins and S.J. More (2005). The impact of badger removal on the control of tuberculosis in cattle herds in Ireland. Preventative Veterinary Medicine, 67:237-266.

Krebs J.R., R.M. Anderson, T. Clutton-Brock, C.A. Donnelly, S. Frost, W.I. Morrison, R. Woodroffe and D. Young (1998). Badgers and bovine TB: Conflicts between conservation and health. Science, 279:817-818.

Olea-Popelka F.J., O. Flynn, E. Costello, G. McGrath, J.D. Collings, J. O’Keeffe, D.F. Kelton, O. Berke and S.W. Marin (2005). Spatial relationship between Mycobacterium bovis strains in cattle and badgers in four areas in Ireland. Preventative Veterinary Medicine, 71:57-70.

Olea-Popelka F.J., J. Phelan, P.W. White, G. McGrath, J.D. Collins, J. O’Keeffe, M. Duggan, D.M. Collins, D.F. Kelton, O. Berke, S.J. More and S.W. Martin (2006). Quantifying badger exposure and the risk of bovine tuberculosis for cattle herds in county Kilkenny, Ireland. Preventative Veterinary Medicine, epub ahead of print.

Phillips C.J.C., C.R.W. Foster, P.A. Morris and R. Teverson (2003).The transmission of Mycobacterium bovis infection to cattle. Research in Veterinary Science, 74:1-15.

Primm P., C.A. Lucero and J.O. Falkinham III (2004). Health Impacts of Environmental Mycobacteria. Clinical Microbiology Reviews, 17:1,98–106.

Scantlebury M., M.R. Hutchings, D.J. Allcroft and S. Harris (2004). Risk of disease from wildlife reservoirs: Badgers, cattle and bovine tuberculosis. Journal of Dairy Science, 87:330-339.

Smith N.H., J. Dale, J. Inwald, S. Palmer, S.V. Gordon, R.G. Hewinson and J.M. Smith (2003). The population structure of Mycobacterium bovis in Great Britain: Clonal expansion. PNAS, 100:15271-15275.

Young J.S., E. Gormley and E.M.H. Wellington (2005). Molecular detection of Mycobacterium bovis and Mycobacterium bovis BCG in soil. Applied and Environmental Microbiology, 1946-1952.

V for Vendetta

I just came back from this movie and all I can say is that it's politically heavy handed but overall it's a very good film. There are some things that don't make much sense and sometimes the movie is all over the place, but is overall far from the boredom that the Matrix sequels ended up being. It's definitely worth seeing.

PNAS cover this week

This weeks cover photo for the Proceedings of the National Academy of Sciences (PNAS) is really nice. The photo is of some rat alveolar macrophages taken from the lungs of rats taking up some polystyrene disk particles. I think it's a very pretty looking photo and demonstrates the wonderful function macrophages have in being the 'clean up' crew of the body. The photos accreditation is to Julie A. Champion who is the author of an interesting paper published in that issue of PNAS, which is looking at how particle size and shape affects the uptake of particles by macrophages.



Wonderful photo. As a side note, I would suspect the sample was prepared for a scanning electron microscope and then the subsequent captured image above has been 'colourised' (just like Ted Turner!) by a computer. Normally images that you see through electron microscopes aren't very pretty and are pretty much just all grey.

How evil am I?

You Are 24% Evil

A bit of evil lurks in your heart, but you hide it well. In some ways, you are the most dangerous kind of evil.

How Evil Are You?

A bit disappointing really. It seems that I've fallen well behind in being corrupted by anime, blaming my flatulence on others and evilution. I need to try harder it seems.

Chick tract on chemicals

Jack Chick likes to write comics that tend to generally convey his anger about certain issues or things he finds offensive: just about anything in other words. One of his older comics was on a group of people playing DnD and was basically a huge strawman. I won't directly link it, because Jack Chick deserves no extra bandwidth in general and out of consideration for the mental health and stability of my readers. It is good then that Bronze Dog from Rockstars' Ramblings has come up with a highly amusing 'edit' of the original Jack Chicks comic. It certainly has inspired me to try an "argument ad baculum" on anyone who disagrees with me.

Awesome giant centipede video

I saw this video over at pharyngula and concluded it was too awesome not to provide yet another link to. Essentially this is a video of a >1 foot long giant centipede (Scolopendra) attacking, killing and then devouring a mouse. There is only a few seconds of squeaking after the first strike and then the copious amounts of poison that the animal secretes through its maxillipeds (the part that bites the mouse). It's worth noting for those watching the video (probably with some horror) that the maxillipeds aren't what the centipede uses to eat the mouse. These structures are adapted to secrete venom and additionally kill by impalation (a favoured tactic of other large arthropods like tarantulas as well), but they do have mandibles and if you watch the head closely, you can observe the centipede chewing away on the mouse with its mandibles (under the head).

Centipedes are very underrated killers of the arthropod world. This is obviously the start of an effective (and equally horrible) PR campaign.

Update: I missed it the first time, but also note the spots of liquid that suddenly appear between the joints of the centipedes body as it wrestles with the mouse. I would guess that's actually even more venom, although I've normally only heard of centipedes releasing venom from between their leg joints and not their main segments. That's a pretty awesome adaptation if they can secrete venom that way as well though. It's not entirely without precedent though, the centipedes close relatives milipedes are known to secrete cyanide and other toxic compounds from their joints when harassed.

Plush Kiwa Hirsuta

Remember that furry crustacean that everyone was oogling over from a while back? Well it looks like the obvious thing to do, which would be to make a plush toy of it has now officially occured. I think the toy version looks great and I would most definitely buy one if I ever got the opportunity.

How much does my blog own me?

I noticed that several sciencebloggers did this amusing little test to determine how much their blogs own them. Apparently, this site owns 31.25% of me or something like that. At least it's not a majority share, which I would like to think my passion of science or my obsession with spiders would own the rest of me easily. They can battle it out.

Oh the Onion

I love the Onion, which is so good at satire that sometimes people mistake articles from it for the real thing. Usually they manage to hit home on various points or just make a particularly funny joke. The latest edition has the following 'brief' about a chicken interviewed about having Bird Flu:

DILLON, SC—A chicken at Perdue Farms' Dillon plant downplayed reports of illness Tuesday, saying she was feeling much better. "I might have had a touch of some sort of flu, but I'm over my fever and keeping the ol' corn down. B'cawk!"

I suspect that the chicken wouldn't have even got past the first few sniffles with the current climate about bird flu. Speaking of bird flu now I think of it, if you haven't been to Effect Measure lately and read their excellent summary of two papers about bird flu and where it potentially binds onto human lung tissue, I would very much recommend doing so. It's very well written and much better reasoned than the mainstream news reports, which seem to always miss the key points.

What makes Mycobacterium bovis such a problem?

Part II: Mycobacterium bovis, the English bovine tuberculosis outbreak, badgers and the culling debate.

Mycobacteria represent a large group of incredibly tough environmental bacteria that have in many cases adapted to be successful pathogens, which are classically very slow in killing their victims. One such mycobacterial disease is tuberculosis, caused by Mycobacterium tuberculosis, which is probably one of the oldest described diseases known to man. The hardy organisms have been found to be responsible for the deaths of Egyptian Pharaohs and the disease was often described as “White plague” in the middle ages. This was because heavily infected victims cough up an off white frothy substance, packed with M. tuberculosis and blood, called sputum. M. tuberculosis is remarkable in another way; as one of the most significant diseases humans passed to animals (rather than vice versa), in this case to cattle some 6 to 10 thousand years ago. The product of that jump over the species barrier was Mycobacterium bovis, which is today one of the most prevalent and significant pathogens of domestic and wild animals.

Why mycobacteria are such good pathogens

Mycobacteria represent an ultimate trade off between factors that make them highly difficult to kill for the host immune system and yet heavily restrict their own growth. This means that mycobacterial diseases are classically slow taking months or years to cause disease, are usually very debilitating and go completely undetected until it’s too late. Arguably the most important factor for the success of mycobacteria such as M. bovis as a pathogen is their amazingly tough cell wall.

Unlike other bacteria, the cell walls of mycobacteria are heavily composed of lipids that make them extremely tough. This tough wall makes it very difficult for cells of the immune system, like macrophages to break down the organism and M. bovis will survive quite well in microphages. Despite the advantage of higher protection such an unusual cell wall does come with some key trade offs. Their cell wall is not very permeable to many substances, giving the microbe a tougher time acquiring nutrients and the organism spends large amounts of energy synthesizing fatty acids.

Another unusual characteristic of mycobacteria is that they have only one or two 16S ribosomal RNA cistrons (compared to 7 in Escherichia coli). This contributes to the immensely slow growth of mycobacteria as ribosomes are essential in the rapid production of new proteins, so the inability to rapidly produce more ribosomes means the microbes maximum growth speed is pretty much capped. Comparing E. coli to M. bovis is rather like comparing a Ferrari with a broken down jalopy with one wheel missing.

It can take (for example) up to two weeks to grow mycobacteria to useful numbers for an experiment in a lab, compared to one day for E. coli. Although seemingly a stupid idea for the organisms survival initially, it does have two key advantages. It’s very useful against antibiotics that target the ribosome, as only one mutation can instantly make the organism resistant and prevent any real damage. Additionally a slow growth rate makes it very easy to assess a changing situation and adapt to the new situation without committing to an ‘all or nothing’ style scenario.

Finally, mycobacteria are easily aerosolized (so they spread between individuals easily), are taken up by macrophages rapidly and are fairly drug resistant (largely due to their cell wall and their slow metabolism). Worst of all, the large presence of environmental reservoirs of mycobacteria makes an effective vaccination difficult. The current BCG vaccine (Bacillus of Calmette-Geurin) has often been found to be ineffective in providing immunological protection and part of the suspected reason for this is ‘confusion’ of the immune system by environmental mycobacteria.

M. bovis provides a particular threat to farm economies

Perhaps the most prominent reason for the problem with eliminating M. bovis from cattle is the large host range that M. bovis exhibits. As well as cattle and to a lesser extent humans the organism is known to infect badgers, possums, deer, sheep, ferrets, oxen, buffalo, lions and wildebeest. This immensely large host range makes control of the disease almost impossible in areas where there is a wild animal reservoir that can prevent elimination of M. bovis. The large host range of M. bovis is almost certainly a result of its wide metabolism and the fact most mammalian immune systems are pretty similar.

Elimination of this disease in some places of the world, such as New Zealand and the United Kingdom that has animal reservoirs is hence very difficult. Making things worse, the suspected animal reservoirs are also found in close association with cattle that are susceptible to infection. The important question that needs to be answered is what role do these vectors play in the transfer of M. bovis to cattle? Join us back this week for part III: What evidence suggests badgers infect cattle with M. bovis?

References

Primm P., C.A. Lucero and J.O. Falkinham III (2004). Health Impacts of Environmental Mycobacteria. Clinical Microbiology Reviews, 17:1,98–106.

Salyers A.A. and D.D. Whitt (2002). Bacterial Pathogenesis: A molecular approach 2nd edition. ASM press, Chapter 19:291-310.

Previous post by me about the origins of M. bovis. The quoted paper in particular.

Britannica upset with Nature

A while back, Nature posted a comparison of the free encyclopaedia wikipedia with that of the formal published Britannica. It appears that the general conclusion Nature reached, which was that wikipedia was sometimes as accurate or even better than Britannica on scientific articles has struck a nerve. Nature begin their response pointing out what they were accused of:

In our issue of 15 December 2005 we published a news article that compared the Internet offerings of Encyclopaedia Britannica and Wikipedia on scientific topics (“Internet encyclopaedias go head to head”, Nature 438 (7070) p900-901; http://dx.doi.org/10.1038/438900a). Encyclopaedia Britannica has now posted a lengthy response to this article on its website, accusing Nature of misrepresentation, sloppiness and indifference to scholarly standards, and calling on us to retract our article. We reject those accusations, and are confident our comparison was fair.

The original analysis didn't seem to have been flawed in any particular manner and seemed to have been perfectly fair, though I feel Britannica does have a few legitimate complaints in places. Firstly, Nature did only take smaller segments from articles to show their reviewers and often some of the complaints were addressed in the larger body of text. Additionally, Nature seems to have taken material that is from other editions of the encyclopaedia, which are intended for younger audiences or not included in the main edition of Britannica. I do see that as a valid complaint because that would skew the analysis. After-all Nature are implying the wiki gets as accurate as the encyclopaedia Britannica, which is a somewhat different thing than their other publications.

Otherwise, through reading both the responses from Nature and Britannica, it does seem that Britannica were trying to save face and their reputation primarily as many of their complaints, such as shortening articles, were equally applied to wiki articles by Nature. Of course this defensive response from Britannica does make sense, who would want to be beaten out by a free online encyclopaedia that's not even written by experts? This point in particular seems to have got Britannicas goat, as you can see here from the opening of Britannicas response:

In its December 15, 2005, issue, the science journal Nature published an article that claimed to compare the accuracy of the online Encyclopædia Britannica with Wikipedia, the Internet database that allows anyone, regardless of knowledge or qualifications, to write and edit articles on any subject.

Which then moves onto a typical attack that the wiki often hears from its detractors:

Wikipedia had recently received attention for its alleged inaccuracies, but Nature’s article claimed to have found that “such high-profile examples [of major errors in Wikipedia] are the exception rather than the rule” and that “the difference in accuracy [between Britannica and Wikipedia] was not particularly great.”

Arriving amid the revelations of vandalism and errors in Wikipedia, such a finding was, not surprisingly, big news. Within hours of the article’s appearance on Nature’s Web site, media organizations worldwide proclaimed that Wikipedia was almost as accurate as the oldest continuously published reference work in the English language.

This is often a problem with the wiki, particularly on controversial issues like evolution, the holocaust and other contentious articles that are prone to vandalism. Many of the articles on wikipedia are of a very high quality however and are well maintained by individuals with expertise in their fields. Unfortunately, the wiki seems better for "fan cruft" and other similar information like details about popular computer games or anime series than as a scholarly resource at the moment.

In any particular event, I think that Nature probably weren't as careful with their analysis as they could have been originally. Some of the mistakes that Nature claim to have identify in the Britannica articles do not appear to be overly relevant at times (see Britannicas response for some details). Without seeing what the same reviewers thought about the relevant wikipedia articles, it would be impossible to determine if there was any real reviewer bias either way. Hopefully Nature will produce a more detailed response that clarifies how their reviewers went about determining errors and the like. Importantly, I would like to know how Nature decided what parts of the articles to take as that could heavily impact on the end result.

When public health, farm economics and conservation collide

Part I: Mycobacterium bovis, the English bovine tuberculosis outbreak, badgers and the culling debate.

One of the most prominent problems for public health authorities and a countries economy comes from infectious diseases that target farmed animals. There are a wide number of pathogens that affect the animals that we grow as food that present a real public health risk, such as Campylobacter jejuni in chickens, Escherichia coli O7H157 in cattle and mycobacteria like Mycobacterium avium subspecies paratuberculosis in sheep. Control of these organisms often involves improvements in animal husbandry, such as simple measures like keeping animals separated and the use of improved diagnostics or vaccinations. Where these control measures become insufficient is when the disease has other vectors, which are also in high numbers and present unique difficulties in controlling or eliminating. Such is the problem that several countries face in controlling bovine tuberculosis, caused by Mycobacterium bovis a relative of one of man-kinds earliest known pathogens, Mycobacterium tuberculosis.

M. bovis historically was a considerable risk to human health, as the organism is viable in milk and of course in the meat of infected cattle. An inquiry in 1934 determined that M. bovis was responsible for some 2,000 tuberculosis deaths (around 6% of the total, the rest being caused by the human specific M. tuberculosis). Today, M. bovis is not much of a problem in humans, as the introduction of milk pasteurization and particularly tuberculin testing has entirely eliminated bovine tuberculosis as a human and animal health threat. This is because tuberculin testing allows for the identification of animals potentially infected with M. bovis and their rapid slaughter and removal from the herd. This policy has completely eliminated M.bovis from cattle herds world wide, except in certain countries such as the United Kingdom (notably Wales, Ireland and England), New Zealand and the state of Michigan in the United States of America.

The question then has to be asked in what makes these regions so different from the rest of the world? The simple answer (but in reality not so simple answer) is the presence of other animals that serve as a vector for M. bovis. In New Zealand, the principal reservoir is the brushtail possum (Trichosurus vulpecula), in Michigan (USA) it’s white tailed deer (Odocoileus virginianus) and in the UK the Eurasian badger (Meles meles). In each country the test and slaughter method has managed to almost entirely wipe out M. bovis from cattle, drastically reducing rates particularly in the 1950s and 1960s, until around the 1980s where M. bovis makes a massive comeback. In the UK particularly, rates of bovine tuberculosis in cattle have increased rapidly and equally as quickly spread to other farms.

As a result of these vectors, which provide a large reservoir for M. bovis, it makes the typical control methods insufficient to completely eliminate the disease. This means that the continued re-infection of herds previously cleared of bovine tuberculosis becomes a considerable problem, as like its human cousin M. tuberculosis, M. bovis takes its time in causing any visible disease. This means an infected animal can fly under the radar for months exhibiting no particularly visible signs of infection and be excreting dangerous numbers of infectious bacteria in its sputum, feces and other excretions. As a result where M. bovis infection is rampant, there is a considerable economic burden on farmers in terms of more regular tuberculin testing, herd movements being locked down (put on restriction) until they pass two clear tuberculin tests and the overall loss of animals.

As many of you are probably thinking, the best way theoretically to control a vector borne disease is surely to directly control the vector and vectors that prevent the elimination of M. bovis. A particularly attractive option on the surface is to engage in a mass elimination of the potential vector from around farmland, to attempt to prevent contact between the infected vector and uninfected cattle. Unfortunately the way things work in reality is often much more difficult than theory. Compared to the large numbers and difficult terrain that the possums have on their side in New Zealand, in the UK badgers are implicated as the vector and are not particularly difficult to find as they leave obvious marks of their habitation. A large scale cull should be the obvious solution except for one key problem: The British love their badgers.

There is a considerable conservation and animal rights movement in Britain that heavily opposes any potential cull of badgers. As a result the control of M. bovis has become a considerable political football with two sides, farmers who want to cull badgers and animal rights organizations that claim badgers are being used as a ‘scapegoat’. With neither side giving an inch and the decision about the next potential badger cull to come soon; the UK debate about the best means to control M. bovis raises an important question as to how scientists, government officials and the public should interact in the control of infectious diseases.

In solving this, numerous lines of inquiry will have to be explored to determine what the best solution that all sides could agree on would be. Firstly, it is worth looking at the biology and history of Mycobacterium bovis that make it such a successful pathogen. Then in terms of resolving this debate, it’s essential to determine the role that the Eurasian badger plays in the spread and persistence of M. bovis in the UK against other potential factors.

Once the link between M. bovis and the badger as a vector has been established, an analysis to see what benefit (if any) that culling would present on reducing herd breakdowns (confirmed cases of bovine tuberculosis in a cattle herd). Finally an analysis of other potential solutions other than culling such as ‘wildlife friendly farming’ and particularly vaccinating badgers. Finally, after these factors have been considered, we’ll revisit the original question and discuss what sort of compromise between health officials, farmers and conservationists could work.

Join back tomorrow for part II of this series: What makes Mycobacterium bovis such a problem?

Recommended reading

Although I haven’t cited anything in particular for this introduction, there are a lot of papers on this topic and there are a few that are particularly useful in understanding what will be discussed over this week here. If you have access to pubmed or other search engines, a read of some of the following papers would be recommended although not strictly required as they will be discussed in detail as the series goes on:

Donnelly C.A., R. Woodroffe, D.R. Cox, J. Bourne, G. Gettinby, A.M. Le Fevre, J.P. McInerney and W.I. Morrison (2003). Impact of localized badger culling on tuberculosis incidence in British cattle. Nature, 426:834-837.

Donnelly C.A., R. Woodroffe, D.R. Cox, F.J. Bourne, C.L. Cheeseman, R.S. Clifton-Hadley, G. Wei, G. Gettinby, P. Gilks, H. Jenkins, W.T. Johnston, A.M. Le Fevre, J.P. McInerney and W.I. Morrison (2006). Positive and negative effects of widespread badger culling on tuberculosis in cattle. Nature, 439:843-846.

Griffin J.M., D.H. Williams, G.E. Kelly, T.A. Clegg, I. O’Boyle, J.D. Collins and S.J. More (2005). The impact of badger removal on the control of tuberculosis in cattle herds in Ireland. Preventative Veterinary Medicine, 67:237-266.

Gilbert M., A. Mitchell, D. Bourn, J. Mawdsley, R. Clifton-Hadley and W. Wint (2005). Cattle movements and bovine tuberculosis in Great Britain. Nature, 435:491-496.

Krebs J.R., R.M. Anderson, T. Clutton-Brock, C.A. Donnelly, S. Frost, W.I. Morrison, R. Woodroffe and D. Young (1998). Badgers and bovine TB: Conflicts between conservation and health. Science, 279:817-818.

Phillips C.J.C., C.R.W. Foster, P.A. Morris and R. Teverson (2003).The transmission of Mycobacterium bovis infection to cattle. Research in Veterinary Science, 74:1-15.

Carnival of the wee animacules

Although I'm a little late on this one, the carnival of the wee animacules has been posted at Science and Politics.

Canwest apologises

Canwest who own the TV station C4, which boldly decided to show the South Park episode "Bloody Mary" that offended just about every Catholic in New Zealand, has decided to apologise.

Broadcaster C4 says it is very sorry for any offence it caused by showing the controversial South Park Bloody Mary episode.

In a statement the broadcaster says the Standards Committee did not uphold any of the formal complaints it received about the show, which showed a statue of the Virgin Mary menstruating.

But C4 chief operating officer, Rick Freisen, sincerely apologised for any offence taken and said the broadcaster would not repeat the episode even though it is allowed to do so.

I'm so very convinced that they are being very sincere and that it isn't due to other factors like potential boycotts or similar. In any event I must pass my congradulations to C4, seeing as they've happily decided to donate whatever spine they may have had and I can assure you, spines are something that is hard to come by in the media these days. Maybe someone else can find a use for it.

[Note: No offence to our invertebrate masters is intended by this post]

Bloody trackback spam...

I've had to delete over 30 assorted trackbacks from various sites spamming online poker to irritable bowels anonymous or something. I'll take it as a sign that I must be getting popular.

Bioessays journal editorial and reflections

Thanks to PZ Myers, I was introduced to a journal I had not encountered before called Bioessays that I've become a dedicated reader of ever since. They often publish some interesting evolutionary hypotheses, particularly on subjects of my interest such as the immune system and origins of vertebrates. Recently, the editor Adam S. Wilkins has decided to write a piece about Intelligent Design and how scientists should approach the subject. I particularly like his concluding paragraphs, which I'll quote here as the paper probably isn't free and I think he's made a very pertinent point:

Furthermore, those scientists with passionate anti-religious convictions should accept that Science can no more disprove the existence of a Deity or immortal souls than religious people can prove the existence of either. More tolerance of private religious belief, coupled with insistence on what scientific evidence does actually tell us about the history of the world and living things, would be appropriate.

If, in contrast, scientists insist on atheism as the only ‘‘logical’’ belief system or demand that people choose between ‘‘evolutionism’’—the quasi-philosophic belief in evolution as a guide to what should be—and belief in God, the outcome is not in doubt. More than half the people in the U.S. would choose religion and reject the science. The consequences of this would be far wider than simply the confusion of school children about the history of life on this planet. Once one has rejected scientific evidence for an ancient Earth and a long evolutionary history of living things, it becomes correspondingly easy to start denying other scientific evidence, for instance evidence on climate change, resource depletion, the nature of pandemics, the causes of species extinction and much more.

I fully agree with this with the caveats that we shouldn't be afraid to admit that many prominent atheists do think that evolution strengthens their position. For example, Richard Dawkins (who always seems to come up) has stated that "Darwin made it possible to be an intellectually fulfilled atheist" and Paul Myers from Pharyngula has written several pieces on how he feels, which I recommend reading incidentally. This is usually used as some sort of launching point that all evolutionists are atheists and that evolution degrades religious beliefs blah blah blah froth at the mouth blah blah whatever. I think some introspection here might be of some use.

Here's a little story for those who are interested in reading a bit of (probably somewhat incoherent in places) rambling about my reasons for my faith. About 6-7 years ago after probably one of the worst years of my entire life, I lost my faith in God and rejected Christianity completely. I really was a very bitter and angry fellow at the time, having felt that God had deliberately tried to do me in, my family, my friends and virtually everyone else I knew. Because of these rather bad experiences and my already considerable dislike of religion that had been building for a while, I became what most would identify as a "strong atheist". My atheism at the time was directly the result of what I saw around me, such as problems with family members and friends, the world in general and my general angst as an angry young man (And I mean angry).

Science never really came into the picture for my rejection of Christianity and God at the time. You could attribute that to more to general angst and general disillusionment with religion. In fact, I probably wouldn't have cared less about what science had to say on the nature of God because having gone to a Catholic school, nobody ever introduced me to the concept that religious concepts would be directly contrary to science anyway. This of course never became overly relevant, because even with my initial introductions to creationism of the full YEC variety on university bulletin boards and with someone handing me Behes Black Box in my first year of university. Although I only had a relatively poor grasp of science at the time, there was something that never quite made sense with the arguments of the YEC creationists/stealth creationists that I debated with.

I have to concede that creationism merely reinforced my atheism at the time. In fact, I thought Christianity was more ridiculous after encountering creationism than I ever had before. Yet, although this might sound somewhat odd after what I have written just now, I did inevitably regain my faith in God and am unashamed to admit that I'm Christian. Bearing in mind that I was formerly Christian, then became an atheist and now went back, this would seem to make me a 'flip-flopper' I guess one could say. The main thing that made me rethink about things was the Christians I met at University during my second year (and beyond).

I've always been one for actions rather than anything else and I was very impressed with the Christians I met. I found they weren't the general hate mongers that I had frequently come to associate with Christianity like Fred Phelps and Pat Robertson. Many of them are among my best friends still and people who I probably get along best with. I also lost my impression of general Christian bloody minded fundamentalism from my association with these people. I found that many Christians hold a wide range of views on various topics, including scientific ones like evolution, social issues and about the bible itself. Most importantly, I liked the attitudes of many Christians I met, the way they treated others and the fact they still retained a genuinely held belief in God that I once had.

After a lot of reconsideration, I came back to God after careful introspection and decided that many of the core beliefs of Christianity still made sense to me. I should point out that I've never regarded the bible as literal and in particular I've always regarded many stories in the bible as being allegorical or poetic in nature to demonstrate a point, but not be literal history (where they simply fail to make sense, despite what creationists may protest about). In many regards however, I never allow my faith in God, based entirely on reasons from my own introspection to hinder how I view or observe the world around myself. I keep my science as science and God as faith, which I soon found after asking various Christians I met was not an uncommon view.

And so in the end I came back to God and I can even say that I have a more strongly held faith than I did before I lost it originally. This is probably because of the fact I've had a longer time to think about things, but also because my knowledge and general opinions have matured a lot more than what they were. Plus, I'm not as angry anymore, well except when debating where I still can dish out a bit of sass.

I suppose after such a lengthy rant, which was entirely unplanned so it has no real particular point, I should get to whatever it is I'm trying to say. Quite frankly, I don't care if Dawkins (or any atheist) says that evolution allows them to be certain about their atheism. It doesn't particularly bother me, because science isn't something I regard as being in conflict with my belief in God. If I held my belief in God as something that is in conflict with science, maybe I would regard the statements from the likes of Dawkins as threatening and proof of evolution destroying Christianity or some similar nonsense. We shouldn't hide the fact that knowing what is good science is something that a lot of groups, such as atheists, will claim as something that supports their view. Personally, I think evolution and the way nature works is a testament to the power and creative ability of God. Like Adam points out in his editorial that I agree with so much, I can't prove to Dawkins what I believe and Dawkins would have a [probably] impossible time using science to convince me God doesn't exist.

Of course, atheists are almost the 'boogeyman' for Christianity and have been promoted to that spot far too prematurely. I find that it's Christians that are degrading Christianity more than anything else. Those who want to hold concepts like creationism/ID being opposed to decent actual science are doing more harm than they are good, but probably only minimal damage in the end. It's individuals who proclaim that Christians should follow their general bilge and rhetoric like Pat Robertson, Fred Phelps, Kent Hovind and Anne Coulter that do more damage to Christianity than any science ever could. If you ask atheists or those who reject Christians beliefs about the sorts of 'Christians' they have in their minds, they'll tell you about the loud mouthed dribbling of the likes of the above as what their impression of general Christianity is.

The response of numerous Christians demonstrates that not even 'we' like them overly much. There are not many Christians who would like to concede that Fred Phelps, who protests at the funerals of soldiers with his band of escaped lobotomy patients, is a Christian himself. We just shove aside the fact he publicly claims he is Christian, because we know that he isn't following the tenants of Christ in spitting out his virulent spiels about homosexuals or whatever. Unfortunately, he's loud, he's very much in the media spotlight with his antics and these actions speak almost as loudly as the failure of the general majority of Christians to oppose and publicly criticize their ridiculous assertations.

If you ask me what is driving people from churches, making people question their faith and generally degrading the position of Christianity as being relevant in today’s world, it's the lack of moderate Christian voices against fundamentalism.

Blogging this week

I'm a little behind on my reading due to watching the Black Caps give the West Indies what-for in the test matches, so most of the stuff I wanted to write about will be a little delayed. I'm currently looking into the plans to cull badgers in England, which will be the subject of discussion this week and I'm still planning on writing more about the evolution of the immune system (TLRs part II). Other stuff to follow will be more about one of my favourite topics (antibiotic resistance) and I'm looking into alternative theories about what caused the black death as a follow up to this post.

In any event, well done to the Black Caps for a well deserved test series win and without the distractions of the cricket there should be more blogging (hopefully).

Excellent new blog

Good Math, Bad Math by Mark Chu-Carroll is a new interesting blog that covers pseudosciences love of abusing mathematics. I first noticed this blog when Mark did a take-down of the horrific statistical analysis used in the latest paper produced by the Griers at Respectful Insolence. He's since moved onto different subjects now including analysing the mathematics of William Dembski. I highly recommend a read.

Skeptics cirlce posted

The 30th Skeptics Circle is now up and ready for skeptical minds at Paige's Page. This one is quite big with quite a few particularly interesting articles, with possibly a submission from Kelly Jolkowski being one of the best. Essentially, her son Jason has been missing and in her families desperation they turned to 'psychic' help. Unfortunately, she has found that the psychics aren't quite able to live up to their claims and she has a blog dedicated to discussing the numerous frauds and psychic conartists she has encountered. There are numerous other great articles too as always, so head on over and get to some reading!