Tuesday, August 31, 2021

Real World Vaccination Efficacy Update For B.C.


British Columbia has started to release the COVID-19 case and hospitalization numbers broken down into folks who are not and who are vaccinated. Essentially the efficacy is similar to what we noted for Ontario a couple of weeks ago.

First, here are the numbers, per 100K per week (i.e. essentially all for the Delta variant given the recency) as analyzed by the CBC's Justin McElroy:

Thus, the protection is solid for full vaccination with some drop-off for protection for seniors - all of which is good. 

However, again, don't forget that the vaccinated can still be infectious even, potentially, if they are asymptomatic which means that the reason for masking and social distancing is to protect your friends, family members, colleagues and, well, pretty much everyone.

Meanwhile in Florida, concerns have been raised by the Miami Herald that the method of reporting the numbers for the very worst outcome have been changed recently.


The Sweetheart Deal That Destroyed The Little Mountain Rodeo.


The BC Liberal government's Little Mountain sell-off was always about their stupid, phoney made for TeeVee budget surpluses.

Here are Lori Culbert and Dan Fumano from a couple of years ago in the VSun:

...The (B.C.) Liberals have maintained that selling Little Mountain gave them the money to build social housing in other locations, but Postmedia discovered that — because (developer) Holborn hasn’t yet paid for the bulk of the land — the Liberals instead borrowed the money from the Treasury Board and promised to pay it back once Holborn settled its debt...

Now, thanks to a whole lot of work by David Chudnovsky and folk in the neighbourhood as well as Jeremy Allingham and the CBC we actually know just how bad the deal really was:

After 13 years of questions and uncertainty surrounding the privatization of the Little Mountain lands, details of the deal are finally public.

CBC News has obtained the purchase and sale agreement between the provincial government and developer Holborn Properties after protracted efforts through freedom of information processes.

The contract shows that the sale price was $334 million, but the province says only $89 million has been paid by Holborn.

The B.C. Liberal government that was in power at the time of the 2008 deal gave Holborn $211 million in interest-free loans on an 18-year term, the agreement shows. Interest will not accrue on that loan until Dec. 31, 2026...


...Also in the deal was an additional $88 million in low-interest loans for non-market housing, repayable by 2050...


It looks to be pretty clear why the developer worked so hard to make sure the contract never saw the light of day.

As for the super fine members of the government of the day...What, them worry?

Image at the top of the post?...It's from a 2012 2nd quarter budget update from Cookie Dough Mike that made the skullduggery visible for all who wanted to look and dig...Unfortunately, few folks at the time, especially folks  in the local corpMedia, really did.


Sunday, August 29, 2021

Schooled In Rock.


Every once in a while, when the Geezers get together in the garage we try David Letterman's favourite Foo Fighters tune...


And then, when it comes time to play live in front of actual people, we shelve it for myriad reasons including the fact that the drummer has a bit of a problem hitting the big cymbal crashes and fills to his liking during the big build-ups/tempo changes.

Well, given that said drummer is sixty years this kid's senior, I reckon he (and we) no longer have any excuses...

Truth be told, all the geezers are fantastic musicians and, personally, I don't even get what's not quite right about the crashes and the fills...Then again, I'm there pretty much as the mascot and/or the student manager of the varsity team except for the occasional tune that calls for a harmonica break, maybe...


Saturday, August 28, 2021

Who The Hell Is Ken Dahlberg?


In June of 1972 H.R. Haldeman had a conversation with then president Richard M. Nixon and told him that a $25,000 cheque made out to a midwestern Republican party bagman named Kenneth H. Dahlberg had been given to one of the Watergate burglars, Bernard Barker,  by the finance chairman of the Committee to Re-elect the President (the infamous 'CREEP').

We know exactly what was said by both Haldeman and Nixon because it turned up on the so-called 'smoking gun' tape that also included the hatching of the Whitehouse-led conspiracy to halt the FBI's investigation of the Watergate case.

A little later, in July of 1972, Carl Bernstein found out about the cheque from a prosecutor in Miami, Florida but neither he nor Bob Woodward, like Nixon before them, had any idea who the good Mr. Dahlberg was or where they could reach him.

Which meant, of course, that in a pre-Googleplex world, that's when the real work began:
...Woodward asked a Post librarian to see if there was anything on Mr. Dahlberg in the paper’s files. The librarian found a picture of Mr. Dahlberg with (Senator Hubert) Humphrey. Humphrey was from Minnesota. On a hunch, Woodward called information in Minneapolis and got a number for a Kenneth H. Dahlberg. Mr. Dahlberg answered the phone, acknowledged the $25,000 check and, saying, “I know I shouldn’t tell you this,’’ according to the Woodward-Bernstein book, proceeded to reveal that he had given the check to (CREEP finance chair Maurice) Stans...

This is all dramatized to great, if slightly embellished, effect in the movie 'All The President's Men' the result of which is the conversation, in which Mr. Dahlberg is the only major player in the Watergate saga who tells the truth from the very start, shown in the video clip at the top of the post.


I remember when searching for something meant that you actually had to do some actual searching. Heckfire, as an undergraduate it once took me two days of rummaging through library stacks and squinting at microfiche films to find this as the counterpoint to that damnable motorcycle outlaw book by Hunter Thompson, when I should have been instead learning about how ribosomes translate mRNA into protein.

But I digress.

Because what I really wanted to tell you about is how real news people dealt with all of this when they had to be really fast in the days before the interwebz.

And, apparently, one of the best at this game locally was a guy named Warren Barker (no relation to the infamous Watergate burglar - ha!).

Mr. Barker, who ran the then locally-owned CKNW newsroom with iron fists clenched in velvet gloves from 1959 to 1991, died recently and Rod Mickleburgh has written a great tribute to him over at his blog.

Here's the part about Mr. Barker's infamous 'files':

...Barker might have stepped out of a radio version of The Front Page. Pounding the keys on an old typewriter (reporters learned to recognize angry memos by the keys cutting right through the paper), phone receiver cradled on his shoulder, a cheap Old Port cigarillo in his mouth, surrounded by files, he set the city’s news agenda every morning. His only concession to sartorial resplendence was a loosely-knotted tie he hung on the door handle. He would slip it on, whenever he had to meet the station’s “suits”.

Few realized CKNW managed all this with just a small fleet of reporters — two on days, one on nights, plus the incomparable George Garrett. And it was out in New Westminster, far from the pulse of Vancouver. But Barker had a system. It involved endless phone checks (“Anything new?”), cubbyhole newsrooms at city hall and the cop shop, tips from carefully cultivated sources, and the pièce de resistance, a filing system like no other.

In the words of Cameron Bell, who went on from his Barker tutelage to revolutionize local TV news at BC-TV: “In an era before computers, in a newsroom the size of a sedan, Barker would carefully construct ongoing files for ongoing stories. They’d be put away in files for instant recall. Barker could retrieve information faster than the most computerized databases today.”

Garrett, who spent nearly 20 years working under Barker, said his boss kept files on everything. Fire deaths, traffic deaths, court cases, labour stories, status of the Mission River Gauge that measured the annual Fraser River freshet…In fact, just about every story reported on ‘NW found its way into Barker’s extraordinary filing system, in chronological order. “And all before computers,” marvelled Garrett...

Imagine that!

In the movie the embellished bit is the part where Redford as Woodward searches through old phone books stored in the celluloid version of the Washington Post newsroom to find Dahlberg's phone number...Most interestingly, the film's props dept used a version of the Minneapolis phone book that came out a few months after the call was actually made...Which, apropos of absolutely nothing at all, is a fact nugget I would never have found if I had not been trolling the outer edges of the Googleplex earlier this morning...


Friday, August 27, 2021

Call Manipulation What It Is Regardless The Politics.


Last Sunday Cynthia Freeland posted an edited video of Erin O'Toole discussing his desire to introduce a modicum of private healthcare delivery in Canada.

What was removed in the editing was Mr. O'Toole clearly stating that he wished to do this in the context of maintained universal access to care.

Here is what Ms. Freeland tweeted atop the edited video:

Sean Holman, speaking on Canadaland this week, pointed out that the editing itself was not manipulative given that the jump cuts in the video are obvious. 

I agree with Sean on this point.

However, in my opinion, what was generated by the editing process was manipulative given that the video Ms. Freeland linked to in her tweet (and which Mr. Trudeau re-tweeted) strongly suggests that Mr. O'Toole wants to do something that many Canadians feel is bad (i.e. utilize private, for profit healthcare delivery) while simultaneously removing any indication that Mr. O'Toole wants to do this while maintaining universal coverage which, of course, most of those very same Canadians think is a good thing.

Now, you can (and the Liberals should) argue that Mr. O'Toole's strategy of mixed private/public healthcare delivery is a bad one, especially with respect to the likelihood that it will ultimately generate a more costly two-tiered system  etcetera.

However, what the Liberal were doing here was not that.

Instead, they were being manipulative in an attempt to generate a 'gotcha'  propaganda scare amongst a certain slice of the electorate that might be starting to kick the tires on Mr. O'Toole's campaign bus.

Thus, I'm happy that Twitter slapped a 'manipulated video' warning on Ms. Freeland's original tweet, even if Conservative insiders may have been the impetus behind said slapping (scroll down to 'Freeland vs Twitter').

Why am I happy?

Because I think that the only way to make our politics better is to call out this gotcha crap for what it is, especially when it is manipulative, regardless the party and/or politician that initiates it.


And no,
despite the claims of some apologists, Ms. Freeland's posting of the full, unedited video down thread does not absolve her and hers...Why?...Well, ask yourself this...Why did Ms. Freeland not just link to the unedited video in the origina, top of the threadl tweet wherein she notes that our universal healthcare system is one of our greatest strengths?
I was actually surprised that Mr. Holman did not see this as manipulative while he spoke with guest host Fatima Syed on Canadaland's podcast. Sean did say he found it to be biased and further noted that one has to be careful, given worse stuff, often coming from the right side of the political ledger, about trumpeting false equivalencies that lead to problematic claims of 'both siderism'. Ms. Syed on the other hand, while agreeing with Holman's point about bias, laughingly said that we all just want politics to be better after dismissing Twitter's manipulated media moniker. Well, if that's the case...
Mr. Holman also brought up the matter of how problematic Canada's access to information laws and procedures are, including how much hidden stuff should be publicly available without an FOI request...Here, I agree with him 100 percent...We also thank him for drawing our attention to Stanley Tromp's database of media stories that have been generated, at least in part, due to material obtained by FOI over at the BC Freedom of Information and Privacy Association's website.
Finally, hearing Sean talk politics on my non-radio device made me think it was a Sunday morning from days of yore even though it was a Thursday evening bike ride when I actually listened.
Update, late Friday afternoon: Sean Holman expands on  his position in a good Twittmachine thread, here....Clearly, Sean is more hard-headed and realistic about how politics is routinely practiced in this country...Me, I see those practices as a big part of the problem with our body politic and want to see them changed, regardless how unrealistic that might be.


Saturday, August 21, 2021

A Fundamental Change In The Way Election Campaign Races Are Run?


Not sure about you all, but I've always thought of Canadian election campaigns as one continuous horse race where the steeds start out slow, pick up the pace in the backstretch, and then start jockeying and sprinting furiously as they round the final turn and head for home.

And nothing represents that mad dash for the finish line better than when the party leaders go bonkers in a campaign's final days and start crisscrossing the country in an effort to hit as many strategic regions and ridings as possible.

But Greg Fingas, writing over at his most excellent blog 'Accidental Deliberations', thinks that the nature of such races might be changing:
...The provincial elections held in the course of the COVID-19 pandemic have generally seen both a continuation of the trend toward increased advance voting, and a substantial increase in the use of mail-in ballots. But by the time the votes have been counted, the overall turnout hasn't been all that strong.

And that combination of increased early voting and decreased election-day turnout raises important considerations for (a) campaign.

First, it means that persuasion in the opening days of the campaign will actually serve to lock in votes early - or conversely, that a failure to reach people by that stage could put them out of reach for the duration of the campaign. And so even to the extent a party might otherwise be tempted to hold off on messages or platforms to reduce the time in which they can be picked apart, the balance tilts strongly in favour of ensuring that early voters have a chance to see what's on offer.

By the same token, the events which would normally be seen as shaping the outcome of an election - from debates to gaffes to movements behind a particular leader - are all likely to have comparatively less effect than in previous elections due to the votes which have already been banked by the time they would take place.

At the same time, while those most motivated to vote need to be reached with persuasive messages early in the campaign, the voters left to be accessed on election day are then likely to be those who have put relatively little thought into how to vote as a matter of both partisan support and process...


Instead of one long, linear horse race, it appears that we may be moving towards something more akin to the Tour de France, with multiple stages made up of sprints, grueling climbs and daredevil descents, each with their own 'prize' of votes of a different kind.

Which could be fun, especially if it screws up the ability of pollsters and pols figure out what buttons to push and pull for the duration.

At least for the moment, because you know for darned sure that if this change from horses to bicycles really is happening those very same pol(lster)s are already hard at work doing their best to re-slice and dice the demographics so that they can sock away votes at each stage of the new fangled race.


GFingas regularly posts really thoughtful media/blog round-ups from a progressive politics point-of-view that are always worth having a look at....Here's a recent example.
Image and subheader?....This!


Friday, August 20, 2021

Life On The Alberni Inlet.

Last weekend we discussed the short-lived 'end' and subsequent resurrection of the ferry/cargo service central Vancouver Island's Alberni Inlet.

My own personal reminiscences leaned toward that of a tourist with a back pack.

Then our old friend Scotty, who once travelled the ferry regularly, weighed in:
"I loved riding the Lady Rose back in the day. The frail, weathered skipper in elegant white turtleneck and navy reefer patiently instructing his first mate for the cameras (The burly, silent “August” probably needed no instruction about hoisting pallets out of the ship’s hold). Our toddler daughter transfixed by dolphins surfing alongside the prow. The milk run deliveries at the Kildonnan dock as so many tourists flocked to snap photos of crusty old loggers picking up cargo that the Lady Rose listed considerably—and August silently adjusted the block pulleys accordingly. I worked in the woods along the south side of Alberni Inlet. We’d take the Lady Rose down to Bamfield or Ucluelet for vaycay. It was a wonderful time"

You know what?

Sometimes I think that maybe Scotty is the holder of the people's history of everything when it comes to lives lived in the westcoast woods.

Image at the top of the post...The Kildonan dock, circa 1929, which probably even pre-dates Scotty's first arrival there.


Thursday, August 19, 2021

An Interesting Bit Of Cell Biology With Variant Spike Proteins.


Sequencing the nucleotides of genes allows you to determine the coded for sequence of amino acids  in the protein concerned.

As a result, changes in the nucleotides in the gene sequence (i.e. mutations) lead to changes in the amino acids in the protein. Such changes are how the SARS-Cov-2 viral variants are generated.

Once the amino acid sequences are known that structural biologists jump in and try to figure out how changes in variants alter protein topology and, potentially, the way the protein works.

But, even with all this important and elegant 'molecular' work, the next step is to test the function of those mutated/changed/variant proteins in cells.

And a group from Boston has deposited a pre-print wherein they present some interesting data with the various SARS2-Cov-2  S-protein variants.

One of the interesting things these folks did was make funky 'pseudo' viruses that are decorated with the various S protein variants from SARS2-Cov-2. They then looked to see how fast those variants decorated pseudoviruses fuse with cells expressing the ACE2 receptor on their surface.

Here are the data which show that the Delta variant S protein (red line) causes more rapid membrane fusion in their experiments:

This group also did this with cell-cell fusion which led them to make the following conclusion:
...Our findings from both cell-based and pseudovirus-based assays suggest that the Delta variant can infect a target cell substantially more rapidly than the other variants we tested, either by more effective attachment or faster fusion kinetics...

It will be very interesting to see if this finding holds up and if it explains, at least in part, why the Delta variant virus is more infectious in people.

Again, while I'm a biologist our group does not do research on viruses....We do, however, develop all kinds of assays to test gene/protein variant function in various cell models.


Tuesday, August 17, 2021

Danny Says...


Danny says we gotta go...

And then, in the end, so did he...

The Danny here is former Ramones co-manager Danny Fields, who apparently took the picture at the top of the page...I have no idea who the geezer is in the bottom picture...It could just as easily be Roger Stone as it could be Mr. Fields, who's still alive in kicking. Then again, maybe it's the ghost of Tommy Erdelyi.
As for the tune of the post title...This!...and This!...and, maybe weirdest and most wonderful of all, This!


Ontario Is Releasing The Data Daily...

Ontario is releasing data on COVID cases, hospitalizations and ICU stays among the unvaccinated and vaccinated, daily.

And the Star's Ed Tubb has been tracking it. Here his summation from yesterday:

Quite the difference, no?

And it supports up our earlier 'Five things you can explain to the truly vaccine hesitant' post from last week.


Sunday, August 15, 2021

The Apparent End Of The Port Alberni To Bamfield Ferry Service.


Update: Looks like the service has been saved!

Our Dad first took us on the Westcoast Trail in 1973, I think.

Back then there was little boardwalk and very few cable cars crossing over rushing water which meant that there was a whole lot of, as my younger brother, later the fireman, said at the time 'Mud a blowdowns!' as well as raft building for the fording of swollen creeks*. 

Given all this we decided that the only way that sane people travelled the trail was to start from Port Renfrew and trudge from south to north to get the worst of the thing behind you during the first few days before it all got a little easier once you crossed Nitinat Narrows, hung out at Tsusiat Falls for a bit, and then started heading towards the end at Bamfield.

I honestly can't remember if it was the first or the second time after finishing the trail that we took the trip on the M.V. Lady Rose, the old Glasgow-built combination people/cargo ferry, from Bamfield down Barkley Sound to Port Alberni on the way to civilization re-entry. 

The Lady Rose herself was taken out of operation about ten years ago and she sat tied up on the Tofino docks for quite awhile before she was towed over to Sechelt where a bunch of folks, spearheaded by a guy named Dick Clayton, are hoping to restore her.

But the ferry service itself is still going, using a different ship, the M.V. Francis Barkley, under the auspices of the Lady Rose Marine Services.

Still going until the end of the month, that is.

Susie Quinn wrote that story for the Alberni Valley News recently. Here's her lede:
An icon of Vancouver Island’s West Coast is poised to take its final voyage.

Lady Rose Marine Services will close its doors as of Aug. 31, after 75 years of freight and passenger service down the Alberni Inlet.

The company is yet another victim of the coronavirus pandemic and the economic strain of extended closures and restrictions, owner Mike Surrell said Monday, Aug. 9. The company posted a brief statement on its Facebook page after rumours started circulating about the closure.

“Seventeen months of basically no income going into the winter, which is traditionally slow…maintaining and running these vessels is very, very expensive,” he said.

“With COVID-19 we managed to hang on for 17 months. We’re not able to maintain this pace. Unfortunately, the Frances Barkley will stop sailing at the end of the month.”

Surrell bought the company and all its operations in 2008. He said while COVID-19 was the final strike, it has also been difficult finding employees with the proper certification to help keep the ship running. Working as a mariner is a specialty, and government regulations demand a certain amount of current training and certification...

Here's hoping something can be worked out for all those affected that decreases the impact of this latest development - There is a road up the inlet** but it is not great and there are remote stops that will likely lose their regular, scheduled goods delivery service pretty much entirely.


Don't get me wrong, based on the evidence, I'm still all in favour of getting as much of the population vaccinated as possible, invoking vaccine mandates in situations where folks will be interacting, indoors in close quarters, and to practice social distancing + masking + rapid testing when your interacting with folks outside your pod. However, unless things go completely off the rails due to new data emerging regarding the Delta variant or the wide, rapid spread of a new even more problematic variant (which doesn't look like it will be Lambda), I would be concerned if any future hard lockdowns were not geographically targeted and for as short a duration as possible. After all, we are not, unfortunately, not New Zealand.

Lastly, it really is important to understand and have empathy for a whole lot of folks, including small business folks, who have been truly negatively impacted by the steps we've taken, especially pre-vaccine, to deal with the pandemic so far. This is something that has to be kept in mind as the PHO and we all struggle to choose the best and most prudent way(s) forward.

*The bare bottomed, pack-over-the-head crossing of the Cheewhat River, before they built the bridge, by my youngest brother, later the musician, would come on the next trip. 
**For one of our trips home from Bamfield our Mom actually drove that road, I think in the VW (notso) microbus, to pick us up. We probably still owe her for that one.
And here's something crazily modern, and I'm not sure actually good...Big chunks of the trail can now be traversed virtually via Google Street View...
Tip O' The Toque to reader E.G. for the heads-up on the update.


Saturday, August 14, 2021

The Tiny House And The Company Town.


By now you have likely heard that the billionare who has both taken and railed against the kind of government subsidies that have helped enrich he and his has given up a big whack of his worldly possessions and moved into a tiny house in Boca Chica on the Texas Gulf Coast.

Which is all fine and good as far as it goes.

But one thing you may not have heard is that Mr. Musk's rocket ship company, whose end product is most decidedly not carbon neutral, owns pretty much the entire town.

Christopher Hooks had that story recently in Texas Monthly:

Boca Chica village sits in the shadow of the SpaceX compound. Just a few years ago the village was little more than two streets of a few dozen one-story houses and a shrine to the Virgin Mary...


...After 2018 the company built infrastructure on all three sides of the village: a solar farm to the south, a company-run RV park with chic Airstream trailers to the west, and storage facilities to the east, behind the shrine to the Virgin. Agents for SpaceX urged the villagers to sell quickly while the county officials publicly warned that eminent domain could be used if they refused. Some residents say the offers were not generous, though they were coming, indirectly, from one of the richest men on the planet. Some accepted the buyouts because living under the shadow of the company had become so onerous. “It was as if I didn’t own my own home,” said Cheryl Stevens, who sold her house in 2019...

{snippety doo-dah}

...Today, what’s left of the town exists in a strange kind of superposition between the old and the new, Boca Chica village and Starbase. Some houses—eleven, by Garcia’s count—are still owned by the old residents, gently worn and painted in earth tones. The rest have been repainted black and white and gray. All the new homes sport Tesla chargers in front...


Because Jimmy Durante's final friends were right!

Photo at top of the post...Space-X's kerosene burning booster rocket pile that powers the 'Falcon Heavy' from the AP via the LA Times.


Friday, August 13, 2021

Music To A Science Geek's Inbox.


Our latest paper has been a real battle with the reviewers.

When we first submitted it earlier in the new year the reviewers were generally supportive but they had a lot of questions and concerns. They also asked for a significant number of new experiments before they would decide if our conclusions are truly supported by the data presented. 

That last one is the crucial bit - and that is really the job of concscientious peer-reviewers who are also experts in the field to ensure that the decision is made with rigour.

Of course, any and all  high-faluting 'this is just how science should work' talk was no consolation for the grad student and the post-doc that had already done a lot of work and who would now have to do even more slogging.

Which they did over a period of months. And the revised paper we sent back the journal, with reams of new data and a 12 page, single-spaced rebuttal to the original reviews (which was my job), was much, much improved.

Anyway, that revision went in a couple of weeks ago.

And then, late yesterday, an Email arrived from the editor. The following was buried under the lede:

Reviewer #1 (Comments to the Author):
The authors thoroughly answered all my concerns.

Reviewer #2 (Comments to the Author):
All of the revision changes are acceptable.

Reviewer #3 (Comments to the Author):
The authors addressed and resolved all my concerns raised in the first review.

The upshot is that the paper is now, finally, 'in-press'  and it will be published once we complete the final administrative and editorial (i.e. not scientific) revisions, which I'll work on next week.

In the meantime, this is usually the point in the process where that grad student and that post-doc that did so much of the work on the revisions would get to shoot champagne corks down the long hallway outside my office.*

Here's hoping we can all get together to do that, for real, in a few weeks.

*During the post-acceptance, paper-in-press celebrations my job is to wait about halfway down the hallway, hidden in the alcove entrance to the lab, while the kids who really did the work shake the bubbly and pop the corks.. An angle slightly above horizontal seems to be best as the goal is to send the corks flying, jumping and rolling as far down the hallway as possible. That's when I pop out with a sharpie in hand (green is best/lasts longest) to mark the distance travelled with the person's name, the paper, and the year down low where the wall meets the floor...The farthest mark ever, about 60 feet I reckon, was generated by a kid in 2010 who no longer is one (a kid I mean)...In fact, he has a lab of his own now in the Canuckistanian center of the universe and I'm pretty sure he has already started stealing grants that might otherwise have been meant for us (which is just as it should be, of course).


More Good News For Folks Who Got The AZ/mRNA Vaccination Mix And Match.


From the abstract of a paper by a German group published in the Lancet, yesterday:
...The heterologous (mix and match) ChAdOx1 nCov-19–BNT162b2 (AstraZeneca/Pfizer) immunisation with 10–12-week interval, recommended in Germany, is well tolerated and improves immunogenicity compared with homologous ChAdOx1 nCov-19 (double AZ) vaccination with 10–12-week interval and BNT162b2  (double Pfizer) vaccination with 3-week interval...

So that's good, from a personal point of view, for those here in British Columbia that made that choice.

But it could also turn out to be good from a larger, global point of view as well.

Again, from the expertly peer-reviewed, published paper cited above:
...Heterologous (mix and match) vaccination has been widely discussed to mitigate intermittent vaccine supply shortages and to improve immunogenicity and efficacy of existing COVID-19 vaccines. Our study offers real-world evidence supporting the safety and immunogenicity of heterologous ChAdOx1 nCov-19–BNT162b2 (AZ/Pfizer) vaccination, which is currently recommended in several countries...

On those points #3 and #4 that could be clearly and consistently explained to help the vax hesitant make the right choice (i.e. protection for those who suffer breakthrough infection from developing severe illness), Ed Tubb of the Toronto Star has had a look at the latest unvaxxed, partially vaxed, and fully vaxed hospital and ICU numbers from Ontario. The level of protection, from a whole population perspective, for fully vaxed vs. not vaxxed are startling (10 fold better for hospitalization, 50 fold better for ICU).....Importantly, these ratios are not age adjusted which, as Mr. Tubb points out, likely means the protection ratios are likely even better for those not at high risk due to advanced age.


Thursday, August 12, 2021

There Are Some Things That Should Not Be Crowd Sourced...

...And this is one of them, especially by a medical doctor and a member of the ruling federal government.

To be fair, much of the rest of Dr. Fry's recent timeline, excluding the slew of tweets that are run-up to election announcement-type stuff, is solid and factual regarding COVID-19. 

An update on COVID-19 from Dr. Eric Topol, in terms of vaccine protection against the Delta variant is important...The data on the solid protection from severe illness has not changed, but the protection against break through infections has decreased probably to ~50% protection based on a number of studies from different jurisdictions...It's here.


Wednesday, August 11, 2021

Your Evening Audio...If I Could Only Fly

This one is the cover of a tune by a guy named Blaze Foley who lived on the edges of the Austin outlaw country/folk music scene before he died tragically, way too young, at the age of 39.

Mr. Foley is pictured, above, with Townes Van Zandt at the Austin Pickers festival in 1984 . By that time, both of them, unfortunately, were already past their prime...


What Would Happen If The Freedom To Be Dumb Was No Longer Free?


It would appear that the members of the German citizenry who have made the choice will soon find out.

Kate Connelly has the story in the Guardian. Here is her lede and a wee bit more:
Germany’s leaders have set out new coronavirus regulations for the coming months, including abolishing free rapid testing to incentivise people to get vaccinated...


...The system of free rapid coronavirus testing, which has been widely available for months and has been used by Germans to get into venues such as theatres and football stadiums, is expected to be abolished from 11 October. After that, those who are unvaccinated – except for pregnant women, children or those advised against getting a vaccine on medical grounds – will have to pay for the tests. The hope is that people will no longer rely on the test system as a way of avoiding getting a vaccine...

Of course, as you might expect, the usual suspects (i.e. those who normally long for market-driven solutions to pretty much everything) are upset:

...Among the most vocal opponents are the pro-business FDP party and the right wing populist AfD. One of the AfD’s leaders, Alice Weidel, on Tuesday accused the government of “threatening to split society”...

Go figure.

Sub-header got you humming?...This!
Meanwhile, why are media organs like the Washington Post adding fuel to the USian Covid pyre by publishing the demonstrable codswallop of Ted Cruz and Rand Paul?


Tuesday, August 10, 2021

It's A Thin Line Between Madness And Morans.


From one of the best of the old-timey members of USian Left Blogistan, Maha, getting to the heart of the political anti-vaccination matter down south:
...The implicit message coming from Republican leaders in these parts is that if you’re really smart and thinking for yourself, you don’t get vaccinated. That’s what sheep and libtards do. If you do get sick, you’ll be fine, so what’s the deal?...

Meanwhile, up here in Canuckistanmikitaville, a self-declared owner of the libtards, a fine fellow named Maxime Bernier went North last week, to North Bay Ontario to be more precise, and started babbling on about how it was fine for folks to call him Mad Max because, among other things, he has the 'data':
The Leader of the People's Party of Canada continued his Mad Max Summer 2021 Pre-Election Cross-Canada Tour with a stop at Lee Park near the shores of Lake Nipissing in North Bay Sunday afternoon.

Bernier was surrounded by many anti-lockdown supporters as he expressed his frustration.

He says he is angry.

"You can call me Mad Max," he stated...


 ..."We have the data for over a year, and that is why I believe that I am the only leader of a national party that says 'no' to the COVID-19 vaccine," he exclaimed...

The good Mr. Bernier also told a few folks in a park about how important not getting vaccinated is, because freedom, etcetera, which the small town hyperlocal media organ 'BayToday' promptly regurgitated, pretty much whole.

Which is all fine and good as far as it goes.

But here's what I don't get...

Why did 'real' bigtime news outlets like, say, CTV, CBC, Global, the National Post, the Montreal Gazette and a whole bunch of other print media organ grinder monkeys, none of which I will link to here, also wurlitzer this public health-damaging swill from Mr. Bernier?


There is, of course, a different way to deal with this media strate(r)gy that is premised on getting attention for the spouting of stupidity, and it has nothing whatsoever to do with forcing the break up of the Book of Faces and/or banishing Mr. Zuckerberg to a drab dorm room with perpetual dial-up for life (not that that either of those would necessarily be a bad thing).

Instead, all those big media-on-the-mat organs could just take responsibility for their own actions, make like the Cleveland Plain Dealer, and just say no to candidates and politicians who traffic in demonstrable codswallop.


Subheader?....It's historical.


Monday, August 09, 2021

What To Tell Folks Who Ask About Vaccines And The Delta Variant.



Update: Aug 12th...Regarding points one and two, below...Eric Topol has aggregated the data from a number of studies on vaccine protection numbers against the Delta variant...They are dropping to approximately 50% protection...The protection against severe disease, and worse, however remain solid.

As we predicted a couple not long ago, the American CDC's concern about vaccinated folks who suffer breakthrough SARS-CoV-2 infections that are themselves infectious has muddied the public perception significantly, thanks in no small part in my opinion, to the media's inability to walk and chew gum at the same time.


Let's say you run into someone who is hesitant and you want to calmly explain to them why it is still a very, very, very, very good idea to get vaccinated.

You could try the following five point plan...

First, yes, it is true, vaccinated folks who suffer breakthrough infections of the Delta variant (which is now dominant in North America) can be infectious.

Second, as is clear from the chart directly below from San Diego county, where slightly more than half of folks are fully vaccinated, far fewer vaccinated folks suffer these breakthrough infections:

Third, many fewer folks who are vaccinated and suffer breakthrough infections go on to get sick enough that they have to enter hospital:

Fourth, many fewer folks who are vaccinated and suffer breakthrough infections, who then go on to get sick, actually die. San Diego also has these data, but the graph below is more of a zoom out, done by the Wall Street Journal (paywalled), looking at America's truly tragic real world vaccination experiment county-by-county:

Fifth, getting vaccinated doesn't just protect you but it also protects everyone else in your household, your workplace and your community as well as your loved ones because it decreases spread as was demonstrated by home grown modellers in British Columbia modellers recently:

If you want a nice summary of all the data for all the vaccines, Eric Topol, who really tracks all of this stuff and is a fantastic Twittmachine follow, has it.
Again, please not that, while I am a life scientist, I am neither a virologist nor an epidemiologist...In the spirit of full disclosure, however, I am acquainted with a couple of the home grown modellers cited above.


Sunday, August 08, 2021

Science Sunday...A Potential Role For Natural Killer Cells In Suppressing Metastasis.


One of the big deals in cancer research these days, for good reason, is the concept of immunotherapy.

When you hear about this stuff it usually involves the immune checkpoint inhibitors like, say, nivolumab* which is a monoclonal antibody (the 'mab' part at the end of the name) that binds to and blocks the ability of 'checkpoint' molecules to suppress cells in the immune system, especially T-cells, from doing their job. Thus, these checkpoint inhibitors help the patient's own immune system to get going so that it can attack the tumour cells that it recognizes as foreign.

All of which is great news, and the treatments are getting better and better all the time.

But, still, they only work efficiently in a subset of 'hot' tumours that have lots of immune cells associated with them and that produce the checkpoint molecules, one of which is called PD-L1/CD274**. In addition, these antibodies/inhibitors aren't (at least not yet) very good at stopping the truly awful part of the disease that is metastatic spread.

The metastatic process begins when tumour cells escape from the place where they originate and travel or 'spread' to distant sites. This process is extremely inefficient and, upon arrival at the distant site the tumour cells very often sit dormant and do little or nothing from a pathology point of view, often for long periods of time. The real trouble begins when these dormant tumour cells wake up, start dividing like crazy, and become full blown, life-threatening metastatic lesions.

So, imagine if you could figure out how to keep these tumour cells at the distant site dormant. That knowledge could then be used to develop novel therapeutic strategies to keep the worst cancers in check without having to wallop the patient with classical 'slash and burn' drugs.

There have been a number of tantalizing nibbles on how to regulate tumour cell dormancy and most recently a group from Switzerland published a paper in Nature in June. These folks looked at all the mRNAs that are present in the dormant condition in experimental liver metastases and identified a suite of them that made the investigators think that the tumour cells were being bonked to sleep by a bunch of trigger-happy Woody Harrelson-like immune denizens called natural killer or 'NK' cells. 

The Swiss group then identified the molecule that juices up the NK cells up to do the dormant cell bonking. What's really cool is that  'super agonists' that torque up the activity of this molecule, which is called IL-15, have already been developed. Thus, if this avenue of research can be translated to patients, and the Swiss group already has good 'correlational' data to support the notion, the approach could, potentially, be rapidly moved the clinic.

Man, I dig cell biology, even still, after all these years.

Image at the top of the post is an NK cell in a culture dish getting ready to do its thing...The photo is from that place that Tony Fauci runs.
*The trade/pharma name of for nivolumab is 'opdivo'. There is actually a decent wiki page for it.
**Immunologists love to use acronyms, sometimes without apparent rhyme or reason to outsiders...As someone who is peripherally involved in the field it's a practice that drives me to distraction. In fact, I only half jokingly told a colleague recently that we could help them out with some culture assays as long I didn't have to memorize the 'CD' antigens. She did not laugh.


Saturday, August 07, 2021

All The Westboro Baptist Church Needs Is Love.

Who knew that the goofy-faced kid the Seattle boys brought in from D.C. to play their drums would turn out to be reincarnation of George Harrison.

This is truly amazing...

on the fine folks serenaded by Mr. Grohl and friends can be found...Here.


Friday, August 06, 2021

Your Evening Audio...My Hometown.


Writing about the restoration of Bowker Creek in my hometown of Victoria yesterday got me thinking of this...


Image at the top of the post is the old BC Forest Products sawmill on the Gorge waterway in Victoria  (from the a post by Darlene Newburg on the 'Old Victoria' book of faces page)....Although there is a wee bit of discussion in the comments about which mill this is and where it's located (see comments).


Has The Death Of The Sparkle Ponies Been Greatly Exaggerated?


Perhaps not.

After all, when the Globe(AndNoLongerEmpireMail)'s Editorial Board starts writing gentle eulogies, well...
The history of liquefied natural gas in Canada is littered with multibillion-dollar schemes that churn through years of development but eventually founder when backers realize a project’s economics don’t add up.

Recent examples are big and small.

In March, Chevron abandoned plans for Kitimat LNG in northwestern British Columbia. In July, Pieridae, a Calgary startup, said cost pressures forced it to shelve an LNG proposal in Nova Scotia.

Failing to attract billions of dollars from investors to build an LNG plant is typical, in Canada and elsewhere. The projects are complicated, the global market is intensely competitive and the outlook for future demand is modest.

In some ways, the story of Énergie Saguenay, a proposed $9-billion export plant north of Quebec City that would have shipped Alberta gas overseas, is the same. Backed by GNL Québec, another startup, it was struggling to drum up capital.

What’s different is, on July 21, the Quebec government rejected the plan...


...LNG has been touted by industry and some governments as another windfall to come, one that could even help reduce global emissions. But the veracity of that promise, and the ever-increasing risks brought by climate heating, are rapidly changing the calculus.

If the slide rules in the breast pockets of the Globe's men, and, especially, those of the men that they see fit to please, tell them to stop with the codswallop I reckon that is a good thing.

However, I also worry that some of the fine folks with the most to gain by backing such megaprojects to the hilt, including some local Lotuslandian ones, may perceive/promote an opportunity for the last pony standing.

If you get my drift.

Need a little Lotuslandian context regarding the herd of the formerly shimmering equine mirage?....This.


Thursday, August 05, 2021

Some Things Are Getting Better...Putting Salmon Back Into Victoria's Bowker Creek.

When I was a sullen teenager I trudged daily along side a small stretch of Victoria's Bowker Creek that ran between Oak Bay's high school and the firehall.

At that time, back in the 1970's, the creek was so polluted that it had essentially become an open sewer. And, for most of its path, it was covered over, often with asphalt. Things were so bad that one of the worst things my brothers and I could possibly imagine was being swept into the tunnel shown above that ran under the firehall grounds and the adjacent little league baseball fields.

Things have changed for the (much) better since then thanks to the work of folks like the 'Friends of Bowker Creek'  and the 'Penninsula Streams Society' over the last fifteen years or so.

Which means that the time has come to try and reintroduce salmon into the waterway:
Victoria's Bowker Creek will host young salmon for the first time in decades thanks to the efforts of a local conservation group and Fisheries and Oceans Canada.

The eight-kilometre waterway, which runs through Saanich, Victoria and Oak Bay, is mostly underground but there is an open section in Oak Bay.

The Friends of Bowker Creek Society is partnering with the Peninsula Streams Society to restore salmon to this urban watershed. Fisheries and Oceans Canada has approved the dispersal of 30,000 chum salmon eggs.

Ian Bruce, the executive coordinator of the Peninsula Streams Society, says traditional knowledge and stories suggest there were trout and salmon in Bowker even as late as the 1930s...


Next time I'm in town should probably head on down to that little run of the open creek in Oak Bay and take a short stroll.

And I promise to neither trudge nor be sullen.


Wednesday, August 04, 2021

Carbon Numbers, Plural.


Norm Farrell has an accounting background and he is very adept at going through public accounts to determine what things make us money vs. those that cost us money.

Of course, there are all kinds of reasons, both economic and policy driven, for the change in our fortunes on natural gas.

Unfortunately, the decrease in revenue does not reflect a decrease in the volume of natural gas being pulled from the ground which, in my opinion, is a really big problem, given the still-to-come back end dollar costs. These are the so-called 'social costs of carbon' (SCC) and they continue to climb for any and all fossil fuels no matter how 'clean' and/or 'transitional' they may be.

But what about the non-dollar human costs of fossil fuel-driven increases in atmospheric carbon?

Of course, here in British Columbia we got a truly tragic taste of those human costs a few weeks ago when the heat dome came came down and approximately six hundred people died.


Has anyone seriously tried to model what atmospheric carbon-driven temperature increases will cost us in lives over, say, the remainder of this century?

Surprisingly, the modelling on that has been pretty scanty until last week when a sharp young kid named Danny Bressler published a single author paper on the 'mortality costs of carbon' (MCC) in Nature Communications.

Here is Bressler's kicker, as reported by Rebecca Hersher from NPR:

...When he factored in the latest mortality research, Bressler found that about 74 million lives could be saved this century if humans cut greenhouse gas emissions to zero by 2050, compared with a scenario in which the Earth experiences a catastrophic 4 degrees Celsius (about 7 degrees Fahrenheit) of warming by the end of the century...

Of course young Mr. Bressler* could be way off with his prediction.

But at least work such as his will get us thinking of the human costs of carbon over the longterm as the news cycle ends and the memory of short term events like our recent weekend heat dome begin to fade.

Also, modelling only gets better as more data roll in over time.


Yes, that's Mr. Bressler because he's still working on his PhD at Columbia University.


Tuesday, August 03, 2021

Is There A Way To Prevent The Emergence Of Vaccine-Resistant Variants?

Could a combination of vaccinations and non-pharmaceutical/behavioural interventions that decrease viral transmission rates be used to decrease the risk that new problematic COVID-19 variants will emerge?

First, what their objective was, from the Introduction to the paper:
...(T)o our knowledge, the interplay of the population vaccination rate with the stochastic dynamics of emergence of a resistant strain has been discussed, but not formally modeled. Specifically, a concern is whether a combination of vaccination and transmission rates can create positive selection pressure on the emergence and establishment of resistant strains. To address this issue, we implemented a model to simulate the probability of emergence of a resistant strain as a function of vaccination rates and changes in the rate of virus transmission, resembling those caused by non-pharmaceutical interventions and behavioural changes...

Second, what they found, from the Abstract of the paper:
...We found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment...

So, assuming their modelling has validity, what would be the recommendation for policy makers?

Here's what the authors had to say about that in the Discussion of the paper:
...One simple specific recommendation is to keep transmission low even when a large fraction of the population has been vaccinated by implementing acute non-pharmaceutical interventions (i.e. strict adherence to social distancing) for a reasonable period of time, to allow emergent lineages of resistant strains to go extinct through stochastic genetic drift..."


Even the best models are just that.

However, why not err on the side of caution?

Of course, unlike the U.S. where the real world experiment currently being carried out is one based, to a large degree, on differences in vaccination rates, here in Canada we may soon be doing our own real world experiment that is instead based on differences in non-pharm/behavioural interventions.


Monday, August 02, 2021

America's Very Unfortunate Real World Vaccine Experiment.

Unfortunately, and truly sadly, America and Americans are engaged in a real world COVID-19 vaccine experiment.

The following are the numbers for cases, hospitalization and deaths in the ten jurisdictions with the highest rates of full vaccination as reported by the New York Times for yesterday, August 1st.

And the following are the same categories of numbers for the ten jurisdictions with the lowest rates of full vaccination:

As has been noted recently, the now dominant Delta variant of the SARS-CoV2 virus can be transmitted by both vaccinated and unvaccinated folks. Given this, the percent change in case numbers may become less the issue over time. Regardless, based on the ability of full vaccination to prevent serious illness, the differences in hospitalizations and, most tragically, death rates really matter.

So, regarding hospitalizations, please note that only one of the high vax jurisdictions compared to five of the low vax jurisdictions had an increase of greater than 100% over the last 14 days.

And with respect to deaths, none of the high vax jurisdictions vs. eight of the low vax jurisdictions had daily death rates over 0.1 per 100,000 people. And a number of the daily death rates in the latter category were shockingly high.


Here in Canada full vaccination rates are quite uniform across all jurisdictions, except for a dip in Newfoundland Labrador and PEI. Thus, it is unlikely that we will engage in the same real world experiment with jabs themselves as is occurring in our neighbours and friends to the south. However, it would appear that, unfortunately, we here in Canuckistanmikitaville may be gearing up to embark on a non-pharmaceutical intervention experiment in at least one jurisdiction.  

We can only hope that our full vax rates get to Vermont-like levels before any large increase in case numbers results.

One thing to consider (and perhaps emphasize in the media?)...If dominant Delta variant infections occur among the vaccinated as well as the unvaccinated and if many more folks in the latter group gets seriously sick as a result, who is being most protected by, say, the maintenance of masking?