ISA in B.C.?

There is some explosive news unfolding at the moment.

According to a press release from SFU, “The highly contagious marine influenza virus, Infectious Salmon Anaemia (ISA) has for the first time been officially reported after being found in the Pacific on B.C.’s central coast.”

Wow! Really!? According to the press release, “The virus was found in two of 48 sockeye smolts collected as part of a long-term study, led by Routledge, on the collapse of Rivers Inlet sockeye populations. Dr. Fred Kibenge of the ISA reference laboratory at the Atlantic Veterinary College in P.E.I. made the diagnosis and notified the Canadian Food Inspection Agency (CFIA) of the positive results for the European strain of ISA virus.”

That’s a serious claim to make. Has it been confirmed by the Canadian Food Inspection Agency? Apparently not, we hear.

Yet there is a press conference, a media release and a story already in the Vancouver Sun about this proclaiming that the sky is falling.

This seems decidedly anti-scientific. Announcing you have been proven right before getting full confirmation sounds suspicious. Plus, the host of anti-salmon farming quotes and language in the SFU press release (e.g. the repeated use of the cattle-farming term “feedlot,” which has negative connotations, instead of the neutral “salmon farm”) are surprising for a university-sanctioned press release.

Aren’t universities supposed to be neutral? Aren’t they supposed to be bastions of excellence and prudence?

Even if the two smolts, after further investigation, do indeed show they have ISA and that the samples are from B.C., it’s concerning that the science has taken a back seat to emotion, rhetoric and an obvious anti-aquaculture agenda. Because if they are confirmed, no one will bother to look for any other explanation but aquaculture.

They are making the facts fit the hypothesis.

In fact, science is so far in the back seat here it’s in the trunk. The press release mentions no actual facts other than that two smolts contained the virus. That’s it. The rest is speculation and fear-mongering. We are not exaggerating. Read the press release for yourself and try and spot the scientific facts. There is only one, as we explain above, and even that has not been confirmed as a fact yet.

What is going on here?

We all know why Ms. Alexandra Morton would say this. This is familiar territory for her, and she has been trying to link farms with the decline of wild salmon for more than a decade. Fair enough; but the science has not backed up her doomsday predictions.

Rick Routledge, SFU professor, is a statistician working on a long-term study of Rivers Inlet. He and his team are looking at long-term trends to see if they can find an explanation for the salmon return declines in the region. Why is he involved in this? That’s an interesting question we would like to see answered.

Once we hear if the ISA test results are actually true or not.

Meanwhile, we are aghast that SFU would publish something so flawed as factual, without waiting for science to bear it out.

UPDATE 4:00 p.m. Oct. 17, 2011

Ms. Alexandra Morton was kind enough to publish the lab results on her blog. We have re-hosted them here. They show some interesting information which people reporting on this story need to know.

First and foremost, the samples are tiny. They are tissue samples from sockeye smolt hearts, likely slivers which are usually taken for testing from adult-size fish. To get an idea of how small that sample would be, take a look at this photo:

A sockeye smolt. Source:

Now with that in mind, let’s learn a little bit about how PCR tests work. PCR stands for Polymerase Chain Reaction, and is defined by Wikipedia as “a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.”

PCR tests can be very effective and are now commonly used in all sorts of medical laboratories as well as criminal forensics labs.

However, they have some pitfalls. PCR tests can be highly susceptible to contamination because of the way they work:

It is often said that the most critical source of PCR contamination is DNA from previous PCRs.  Again, a PCR produces many DNA copies of the target DNA sequences.  Due to shear number, these copies (called amplicons) are a hazard for future PCRs.  In terms of DNA typing, stray amplicons could contribute single or multiple alleles to a genetic profile.  This would manifest itself in the form of producing, for example, an extra dot on a DQA1 or PM typing strip or an extra band in an STR profile.  The fact that the contaminating dot or band is in fact extra may or may not reveal itself.  Thus, amplicons can lead to mistyping.

However, a more dangerous source of contamination is what is called genomic DNA.  This is DNA that hasn’t yet been amplified.  Genomic DNA doesn’t have the high concentration of the target DNA copies but is a hazard because genomic DNA could produce an entirely false DNA profile.  Full profile contaminants have been documented on multiple occasions and in multiple laboratories.  Partial profile contaminants are more common and sometimes constitute a poorly recognized risk in using partial profiles in evidentiary samples as evidence.  When contamination occurs there is rarely any way to confirm how it happened.

For example, suppose evidence item #1 has little to no DNA or has DNA degraded beyond the ability to function in a PCR.  Suppose further that item #2 is a defendants reference blood stain that would typically have a high concentration of undegraded genomic DNA from the defendant.  If item #2 comes in close proximity with item #1, or comes in contact with item #1, the genomic DNA from item #2 may contaminate item #1.  Subsequent DNA typing of contaminated item #1 will give the false impression that the defendant contributed DNA to item #1 during a crime.  Similarly, when there are multiple items of evidence with some having larger amounts of DNA and some much lower, cross-contamination is an important consideration.

This is not to say that all PCR-based results are due to cross-contamination.  However, the ease of cross-contamination and its potentially misleading effects may sometimes be under-appreciated, especially in the context of match probabilities reported to be extremely rare.

Did you catch that?

There’s nothing wrong with PCR testing. But if match probabilities show up which are extremely rare, use caution. You may have a contamination issue that needs to be investigated and verified.

So how does that apply to the latest news?

Given the concerns with PCR contamination, and given the extremely small sample sizes, we should be re-testing before announcing to the world that ISA is in B.C. don’t you think?

Unfortunately, according to the lab results, we can’t retest the results or do further investigation because the samples were so small they were all used up.

And this sort of information is what SFU uses to announce “Lethal Atlantic Virus found in Pacific Salmon?”

Once again, real science takes time. But we suppose the personalities behind this announcement couldn’t wait to get their names in the newspaper and couldn’t be bothered to wait for the science to catch up.


Sea lice studies in 2011

Looking through the new science papers published recently we came across this one from the summer titled “Sea lice on wild juvenile Pacific salmon and farmed Atlantic salmon in the northernmost salmon farming region of British Columbia” published in the journal “Aquaculture.”

The abstract is interesting. It  points out that at the low point of sea lice levels during the period studied, the levels of Lepeoptheirus salmonis (the salmon-specific lice parasite) were higher around salmon farms. However, it pointed out that “Over 91% of all the juvenile salmon examined had no sea lice.”

Hm. That’s not a number we’ve heard often. Out of 5,000 juvenile salmon they examined, only nine per cent had sea lice on them?

Full abstract below since Science Direct often changes the link making it annoying for bloggers like us…

Sea lice on wild juvenile Pacific salmon and farmed Atlantic salmon in the northernmost salmon farming region of British Columbia

Sonja M. SaksidaaCorresponding Author Contact InformationE-mail The Corresponding Author, Larry Grebab, Diane Morrisonc, Crawford W. Revied

a British Columbia Centre for Aquatic Health Sciences, PO Box 277 Campbell River, BC, Canada V9W 5B1
b Kitasoo Fisheries Program, 1201-675 West Hastings Street, Vancouver, BC, Canada V6B 1N2
c Marine Harvest Canada, 124-1324 Island Hwy, Campbell River, BC, Canada V9W 8C9
d Centre for Aquatic Health Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada C1A 4P3

Received 21 May 2010; revised 8 July 2011; Accepted 20 July 2011. Available online 22 July 2011.


The Kitasoo/Xai’xais First Nation established a program to monitor sea lice levels on seaward migrating wild juvenile salmon in their traditional territory which contains the most northerly salmon farming region of British Columbia. A total of 12 locations were routinely sampled during the period between 2005 and 2008 to gain a better understanding of the levels and patterns of sea lice infestation on wild salmonids in the region. Over 5000 juvenile salmon were collected and examined for sea lice. Around 78% were identified as pink salmon, 18% were chum salmon and the remainder classified as ‘other’ salmon (coho and sockeye salmon). Two species of sea lice were observed: Lepeophtheirus salmonis and Caligus clemensi. Over 91% of all the juvenile salmon examined had no sea lice and there was no significant difference in L. salmonis prevalence levels among salmon species. However, chum salmon had significantly lower C. clemensi prevalence levels than either pink or ‘other’ salmon. There were significant annual and regional differences in L. salmonis prevalence on juvenile pink salmon; the lowest prevalence in all sampling zones occurring in 2008, while channels containing salmon farms consistently had higher levels than those without salmon farms. Mean prevalence of L. salmonis in the channels with salmon farms ranged from 2% to 9% which is lower than levels published for the same region in different years or for other areas without salmon farms. C. clemensi prevalence on wild pink salmon was associated with sampling zone and the size of pink salmon; larger juvenile fish were more likely to be infected than smaller fish. During the period of wild juvenile salmon migration, the mean abundance of motile stages of L. salmonis on farmed salmon ranged from 0.13 to 0.79 lice per fish but there were no significant differences among years. In comparison, C. clemensi abundance levels on farms were significantly higher in 2005. Factors contributing to variations in these observations are discussed.

For balance, we would like to contrast this with another sea lice study published this year, “Effects of parasites from salmon farms on productivity of wild salmon.” This study’s abstract reaches a different conclusion but provides no numbers. For that you have to read the whole study.

Effects of parasites from salmon farms on productivity of wild salmon

  1. Martin Krkošeka,b,1,
  2. Brendan M. Connorsb,c,
  3. Alexandra Mortonb,d,
  4. Mark A. Lewise,
  5. Lawrence M. Dillc, and
  6. Ray Hilbornf

+Author Affiliations

  1. aDepartment of Zoology, University of Otago, Dunedin, New Zealand, 9016;
  2. bSalmon Coast Field Station, Simoom Sound, BC, Canada V0P 1S0;
  3. cEarth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6;
  4. dRaincoast Research Society, Simoom Sound, BC, Canada V0P 1S0;
  5. eCentre for Mathematical Biology, Department of Mathematical and Statistical Sciences, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2G1; and
  6. fSchool of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105
  1. Edited by William C. Clark, Harvard University, Cambridge, MA, and approved July 27, 2011 (received for review February 2, 2011)


The ecological risks of salmon aquaculture have motivated changes to management and policy designed to protect wild salmon populations and habitats in several countries. In Canada, much attention has focused on outbreaks of parasitic copepods, sea lice (Lepeophtheirus salmonis), on farmed and wild salmon in the Broughton Archipelago, British Columbia. Several recent studies have reached contradictory conclusions on whether the spread of lice from salmon farms affects the productivity of sympatric wild salmon populations. We analyzed recently available sea lice data on farms and spawner–recruit data for pink (Oncorhynchus gorbuscha) and coho (Oncorhynchus kisutch) salmon populations in the Broughton Archipelago and nearby regions where farms are not present. Our results show that sea lice abundance on farms is negatively associated with productivity of both pink and coho salmon in the Broughton Archipelago. These results reconcile the contradictory findings of previous studies and suggest that management and policy measures designed to protect wild salmon from sea lice should yield conservation and fishery benefits.

The first study relies on observational data and makes no claims about what the data means.

The second relies on a lot of mathematical modelling to explain why it is different from other studies which disagree, and concludes that  the previous work of the authors is right.

We leave it up to our readers to consider the differences here, but while we appreciate the work that went into the second study, setting out to prove you were right before isn’t really the basis of a great scientific study, in our opinion.

But the bottom line here in our opinion is that scientists disagree. And that is healthy. Hopefully we will see lots more research and the differing opinions can temper each other, until we get a definitive answer as to whether or not sea lice from farms kill wild salmon.

A reasonable response goes unnoticed

We’ve heard a lot about the “Kristi Miller virus” in the past few months, mostly because that seems to be the only science mainstream media reported on during the Cohen Commission‘s hearings on aquaculture.

What is it? In a nutshell, Kristi Miller is a scientist at Fisheries and Oceans Canada (DFO)’s Pacific Biological Station. She is Head of the Molecular Genetics section. Her name has become well-known in the media since she published a scientific paper titled “Genomic signatures predict migration and spawning failure in wild Canadian salmon” in the journal SCIENCE. Her research found that genetic markers in samples she tested show evidence of a  possible virus which may be associated with higher than normal mortality rates for salmon at sea, and for salmon spawning in the Fraser River.

Let’s back up for a second. What does that mean? It means that salmon with this genetic signature have a greater chance of dying when they go out to sea, or return to the river to spawn.

It DOES NOT mean that there is a virus killing wild salmon. The research doesn’t show that and that is pure speculation. No credible scientists are saying this.

But that hasn’t stopped some people from running with it. “A newly discovered virus could be the ‘smoking gun’ in the 2009 collapse of the Fraser River sockeye,” proclaimed the lead of one media report. Never mind that Miller herself never actually said that (Page 29 Line 8 ):

Actually, I had no intent of saying that
9 in this hearing, that I mean I was a little backed
10 in the corner on that one. And I should clarify,
11 and when I agreed with Mr. McDade that what I
12 really meant was that this could be a major
13 factor. Not the major factor, because I also
14 agree with others that there is no single major
15 factor. And I think that I did put a lot of ifs,
16 ands and buts in at the time that I made that
17 statement. And the main one is that we have to be
18 able to demonstrate that we have an infectious
19 disease, that it causes mortality, that it causes
20 mortality in that early marine phase, because that
21 is where I'm focused on right now, is
22 understanding whether or not we have a viral agent
23 that is highly prevalent when fish, when sockeye
24 salmon are moving into the Fraser River, and at a
25 time when we know from oceanographic data and from
26 the work of Dick Beamish and Marc Trudel that we
27 have highly variable ocean conditions. Okay? And
28 I do work closely with those colleagues.
29 And it is my view that if you take a fish
30 that is already compromised and you put that fish
31 into an environment that is highly stressful, that
32 doesn't have a lot of food, that may not be the
33 optimum temperature, that may have other things
34 like sea lice and other things that they are up
35 against, that you could weaken a fish to the point
36 that they can't -- they simply can't take that
37 level of stress.
38 And I do believe if we are able to
39 demonstrate that this virus does cause disease and
40 mortality in that early marine phase, and if it is
41 activated under stress like it has been shown to
42 be activated under stress in other species, this
43 family of viruses, that there is a potential that
44 it could be associated with high levels of
45 mortality. That does not mean that it directly
46 causes mortality. But if you weaken an animal,
47 you start with a weak animal and then you weaken
Cross-exam by Ms. Gaertner (FNC)
August 25, 2011
it further by poor conditions in 1 the environment,
2 it is the accumulative effect of those stressors
3 that likely causes the mortality that we are
4 seeing in the early ocean environment. That is
5 really what my feeling is on it. I don't think
6 that one factor all by itself has caused this
7 decline.

It seems her correction was ignored by the media, who still stuck to the “smoking gun” cliche in subsequent stories. Miller’s own explanation of her research, and what it means or doesn’t mean, also went ignored by media who preferred instead to quote others who claimed to interpret what Miller said.

What happened to primary sources?

No, really. Isn’t it a journalist’s job to drill down to the primary sources behind a story? Why settle for someone else’s interpretation of events if you don’t have to?

That’s another post though. It just annoys us thinking about it.

This post is about the response to the misrepresentations of science described above. Dr. Tony Farrell, one of Miller’s co-authors on the “Genomic signatures” paper as well as several others, had an opinion column published in the Vancouver Sun on August 27, 2011, only two days after Miller testified at the Commission. It’s reasonable, balanced and makes several excellent points which applies to science from any discipline.

The problem is that we expect too much, too soon from science. The announcement of an “overnight” discovery is always backed by an awful lot of scientific discovery and testing.

While responsible scientists couch their discoveries with words like could, may and might, prudent caution too often gets lost in translation.

Take my salmon research in B.C. as an example.

A news headline early this year claimed a virus from farmed salmon is killing wild sockeye salmon in the Fraser River.

As a co-author of the research cited as the headline’s source, which appeared in the prestigious scientific journal Science, I can safely say our position was far more circumspect. Yet, somehow the headline stretched a discovery-phase hypothesis on a genomic expression signature associated with sockeye salmon to claim a virus had come from farmed salmon! Clearly, this is an illustration of the knowledge gap between science and public perception.

Unfortunately the media, and the public, largely ignored this reasonable response to the hysteria surrounding Miller’s research. Once again, we must point out, Ms. Alexandra Morton has been at the centre of this storm, whipping people into a frenzy and propagating her own interpretation of events. As we pointed out yesterday, she is also taking this research, accepting it as fact, and building her own theory on it, an implausible scenario involving one disease which may have occured on farm in one month of one year killing millions of wild salmon.

That is not a sound scientific approach. Picking and choosing things which fit your pre-conceived opinion and claiming you are then proven right is not good science.

We would like to let Tony Farrell have the last word, since it sums up our position as well:

Have your headlines if you must, because in this fast-paced world we can’t always wait for hindsight, but can we agree to not represent hypotheses – no matter how intriguing – as facts?

Signs of a crank: recognizing pseudoscience

This wonderful list is by well-known skeptic Brian Dunning, who runs the Skeptoid blog. He adapted it from late mathematician Martin Gardner’s book Fads & Fallacies in the Name of Science

It’s surprising, and a little bit frightening, how well some popular, self-proclaimed scientists who work against salmon farming fit these points.

• Cranks tend to work in isolation from their colleagues. This is conducive to drifting far afield. If you want to stay abreast of the latest developments, you usually want to be part of the community. If you’re not, you proceed unchecked, and you lack the checks and balances and corrections of peer review. Isolation is rarely or never the best way to insure that your work is on track.

• Cranks tend to be paranoid. They worry that their important discoveries are being spied upon, that evil forces are out to destroy their reputations, that colleagues are conspiring to suppress their discoveries. Nobody doing legitimate science, or working within the scientific method, has any plausible reason to be paranoid about such things. Can any legitimate scientist recall the last time they conspired to suppress good work?

• Cranks tend to consider themselves geniuses. Cranks tend to learn early on that their work is pretty unique. For some reason they often fail to consider the possibility that this uniqueness is for any reason other than its utter brilliance. “I’m the only one smart enough to see this” a pretty clear red flag. Beware of anyone who claims unique insight.

• Cranks tend to regard their colleagues and critics as stupid. The Dunning-Kruger effect (no relation to me) is expressed when people of mediocre ability are unable to perceive their own mediocrity, and unable to comprehend that others may be smarter or more capable than they. When a crank sees a colleague doing different work or coming to different conclusions, it may well be that his own incompetence prevents him from understanding that it’s possible for others to be smarter. Therefore, the colleagues’ different conclusions can only be due to their stupidity.

• Cranks tend to believe there is a conspiracy against them. Why will nobody publish their paper or invite them to speak at conferences? Is it because their work is poor? No, it must be a conspiracy to protect to status quo and to suppress innovation. A crank is so convinced of his own correctness that there doesn’t seem to be any rational reason for the community to dispute his work, therefore a conspiracy seems to be a better explanation.

• Cranks tend to criticize the work of big names in science. Einstein is usually the favorite. When a good scientist finds a flaw in established theory, that theory rarely happens to be from one of the big names in science; not because the big names are special or infallible, but simply because the huge number of scientists in the world dilutes the big names down to a tiny percentage. Cranks probably tend to go after big names because their own limited expertise makes them more familiar with the big names than with the actual science being done in the field. Have you ever doubted Einstein, at a time when you could genuinely claim to have a thorough understanding of all the work done since his time?

• Cranks tend to invent their own terminology, sometimes their own sciences, and tend to write in their own overcomplicated jargon. Beware of the article that discusses a science with terminology not found on Wikipedia. Beware of any scientist that invents his own name for a new science. Obviously all new sciences do originally need to be named, but the number of crank theories with made-up names is much, much larger. And beware of any article that is written with such jargon in an overcomplicated way that makes no sense. Don’t jump to the conclusion that the author is smarter than you; he may simply be a crank.

The point of this blog is not to assassinate anyone’s character. But when we created our Twitter account this morning, and started following people, we immediately noticed the latest posts from Ms. Alexandra Morton and/or her followers on the “salmonaresacred” account.

We are aware of Ms. Morton and her position, and her work, and don’t plan on singling her out, but this needs to be commented on:

Alexandra Morton: “If ISA virus is in BC, I hope the #salmon farmers and the governments of BC and Canada are insured”

ISA? In B.C.? Of course, we clicked the link which takes us to a long, rambling essay about why salmon farms are killing Fraser River sockeye. There are huge, flashing red warning lights which appear reading the conclusion:

The biology of the fluctuating Fraser sockeye returns is a pattern of exceptional clarity. With healthy sockeye runs occurring in the Columbia River, the sockeye of western Vancouver Island that migrate through Port Alberni Inlet, where there are no salmon farms, and even in the Harrison sockeye which originate from the Fraser River, but avoid the clusters of salmon farms by migrating to sea around southern Vancouver Island, our attention is drawn to the waters off eastern Vancouver Island. It is only the salmon that swim through those waters that are fluctuating unpredictably. The evidence hereinsuggests the unknown variable/s are salmon farm-origin pathogens.

Warning! Warning! Danger Will Robinson! Fallacy alert! First of all, last time we checked, there were salmon farms on the West Coast of Vancouver Island. Are the Harrison sockeye salmon passing by there? Has anyone checked? This is a huge assumption based on an extremely weak correlation.

The sockeye appeared to be dying of a cancer-causing virus that originated in salmon farms on the narrowest portion of the Fraser sockeye migration route. The geography, pathology, flutuations and timing all fit perfectly.

Another warning light should be flashing frantically here.

There is no self-criticism or caution here. Reading through the paper and then through her blog postings it’s obvious Ms. Morton has started with a conclusion and worked backwards; views herself as smarter than everyone else; presents herself as a curator and interpreter of limited and secret knowledge; and will name-drop and cherry-pick whatever it takes to make her point.

No offence meant to her, but this is deeply disturbing, and not just her conclusions. If they are actually true, they should stand up to scrutiny, and should be able to be proved. But given how her conclusion seems to be “there is a huge risk, there is a conspiracy to cover it up, the solution is to stop salmon farming” we doubt there is any real proof for this.

And this certainly seems to fit into the “crank” category. Let’s see how seriously the mainstream media takes it.

Fishy science

It’s alive… it’s… alive!

As alive as a blog can be. Time will tell. But first, an explanation about what this blog is all about, and why we are doing it.

We will write a lot about B.C., Canada because that’s where we live, and like they say, write what you know.

We are unashamedly pro-aquaculture. The population of this planet is going to hit seven billion people in our lifetime and farming fish is a brilliant technological innovation which will help feed them all.

Some people scoff at that. Just like mammoth-hunters probably scoffed at the first humans who collected seeds and planted them in a valley to grow grain for the future. “You’ll never feed your tribe on that,” they may have said. “You have to follow the game, like we’ve done since the beginning.”

There are no more mammoth hunters and no more mammoths. But there are farmers.

Farming is the single greatest technological innovation humanity ever came up with. Without farming, people would have never stayed in one place. They would have never developed growing, healthy, stationary populations. They would have never developed culture. They would never have had time to develop a written language. They would have never had time or the ability to pass those advances on to the next generation. They would have never developed cities, religion, philosophy and all the things which are fundamental to our societies, regardless of where we are in the world.

Farming fish carries on that tradition. Only by using the ocean to farm fish, shellfish and seaweed will we be able to provide enough food for a growing global population.

Are there problems with farming fish? Yes. There are problems and concerns with everything human beings do. But the biggest problem is how poorly and negatively aquaculture has been portrayed in the mass media, particularly salmon farming, which we will likely focus on the most here.

The problem is science, and particularly how people misinterpret it. Sensational, agenda-driven science gets media attention, while moderate and well-researched science gets ignored.

Pardon the pun, but we find that fishy.

We hope this little corner of the blogosphere will help change that, even a little bit, by bringing to light the vast amount of good science which supports aquaculture as a sustainable, good idea.

And before anyone writes us off as biased, we clearly state that we will call BS when we see it, regardless of who publishes it and whether or not it supports our bias. We are no one’s apologist; we’re in it for the science.

Examining the science behind salmon farming

Fish Farming In Beautiful British Columbia

To teach the general public about salmon farms

Alaska salmon's Blog

Salmon Farming and Ranching in Alaska

Transition Times

Writing to Right the World // by Jennifer Browdy

Watts Up With That?

The world's most viewed site on global warming and climate change

Salmon Farm Science

Examining the science behind salmon farming

All the junk that’s fit to debunk.


Protesting the not so peaceful protesters on Vancouver Island