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Last post Author Topic: Peer Review and the Scientific Process  (Read 57082 times)

40hz

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Re: Peer Review and the Scientific Process
« Reply #125 on: February 08, 2015, 07:39:35 AM »
Never mind the New Age movement, astrology, or ectoplasmic production, peer review of alchemy gets you no further, even if Sir Isaac Newton is doing the review. Peer review of Isaac Newton’s physics was rather hard as he was, and remains, peerless in that field.

Yes. But you and I are apparently so brainwashed by government and corporate propaganda and indoctrination that we're now unable to have an appreciation for woo. :-\

The exchange starting around 0:45 on this If Google We're a Guy Part-3 video captures what goes on in my mind every time I get buttonholed by somebody peddling woo who "got 'educated'" as they like to tell you they did. Look for this woman and her question:

woo.png

(Side note: the actress they got in to do Apple's "Siri" is priceless. Watch the whole video plus parts 1 & 2. They're hysterical, to say nothing of spot-on!  ;D)

I have to remind myself what Euripides observed almost 2500 years ago: "Whom the gods destroy, they first make go mad."

I don't have the patience to listen to Mr. Sheldrakes 'censored' talk a third time. Two times was more than enough for me - to say nothing of the 36 minutes and 38 seconds of my life I'll never get back which I invested in order to do so. However, John Baez created a 36-question Crackpot Index to evaluate and rank presentations such as his. I've put it in the spoiler below if anybody with the time to waste would care to take a crack at it. ;)

Crackpot Index
Quote
The Crackpot Index
John Baez


A simple method for rating potentially "revolutionary" contributions to physics:

  
  •    Take an automatic 5 point starting credit. Add:
  •    1 point for every statement that is widely agreed on to be false.
  •    2 points for every statement that is clearly vacuous.
  •    3 points for every statement that is logically inconsistent.
  •    5 points for each such statement that is adhered to despite careful correction.
  •    5 points for using a thought experiment that contradicts the results of a widely accepted real experiment.
  •    5 points for each word in all capital letters (except for those with defective keyboards).
  •    5 points for each mention of "Einstien", "Hawkins" or "Feynmann".
  •    10 points for each claim that quantum mechanics is fundamentally misguided (without good evidence).
  •    10 points for pointing out that you have gone to school, as if this were evidence of sanity.
  •    10 points for beginning the description of your theory by saying how long you have been working on it. (10 more for emphasizing that you worked on your own.)
  •    10 points for mailing your theory to someone you don't know personally and asking them not to tell anyone else about it, for fear that your ideas will be stolen.
  •    10 points for offering prize money to anyone who proves and/or finds any flaws in your theory.
  •    10 points for each new term you invent and use without properly defining it.
  •    10 points for each statement along the lines of "I'm not good at math, but my theory is conceptually right, so all I need is for someone to express it in terms of equations".
  •    10 points for arguing that a current well-established theory is "only a theory", as if this were somehow a point against it.
  •    10 points for arguing that while a current well-established theory predicts phenomena correctly, it doesn't explain "why" they occur, or fails to provide a "mechanism".
  •    10 points for each favorable comparison of yourself to Einstein, or claim that special or general relativity are fundamentally misguided (without good evidence).
  •    10 points for claiming that your work is on the cutting edge of a "paradigm shift".
  •    20 points for emailing me and complaining about the crackpot index. (E.g., saying that it "suppresses original thinkers" or saying that I misspelled "Einstein" in item 8.)
  •    20 points for suggesting that you deserve a Nobel prize.
  •    20 points for each favorable comparison of yourself to Newton or claim that classical mechanics is fundamentally misguided (without good evidence).
  •    20 points for every use of science fiction works or myths as if they were fact.
  •    20 points for defending yourself by bringing up (real or imagined) ridicule accorded to your past theories.
  •    20 points for naming something after yourself. (E.g., talking about the "The Evans Field Equation" when your name happens to be Evans.)
  •    20 points for talking about how great your theory is, but never actually explaining it.
  •    20 points for each use of the phrase "hidebound reactionary".
  •    20 points for each use of the phrase "self-appointed defender of the orthodoxy".
  •    30 points for suggesting that a famous figure secretly disbelieved in a theory which he or she publicly supported. (E.g., that Feynman was a closet opponent of special relativity, as deduced by reading between the lines in his freshman physics textbooks.)
  •    30 points for suggesting that Einstein, in his later years, was groping his way towards the ideas you now advocate.
  •    30 points for claiming that your theories were developed by an extraterrestrial civilization (without good evidence).
  •    30 points for allusions to a delay in your work while you spent time in an asylum, or references to the psychiatrist who tried to talk you out of your theory.
  •    40 points for comparing those who argue against your ideas to Nazis, stormtroopers, or brownshirts.
  •    40 points for claiming that the "scientific establishment" is engaged in a "conspiracy" to prevent your work from gaining its well-deserved fame, or suchlike.
  •    40 points for comparing yourself to Galileo, suggesting that a modern-day Inquisition is hard at work on your case, and so on.
  •    40 points for claiming that when your theory is finally appreciated, present-day science will be seen for the sham it truly is. (30 more points for fantasizing about show trials in which scientists who mocked your theories will be forced to recant.)
  •    50 points for claiming you have a revolutionary theory but giving no concrete testable predictions.

© 1998 John Baez
baez@math.removethis.ucr.andthis.edu

« Last Edit: February 08, 2015, 08:26:43 AM by 40hz »

Renegade

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Re: Peer Review and the Scientific Process
« Reply #126 on: February 08, 2015, 04:31:56 PM »
Marcia Angell is a Senior Lecturer in Social Medicine 
at Harvard Medical School and former Editor in Chief of The New England Journal of Medicine.


 


http://www.nybooks.c...story-of-corruption/

Quote
Drug Companies & Doctors: A Story of Corruption

It's a long article, but it is worth a read for anyone interested in the general topic of this thread.

tl;dr - The Medical Industrial Complex is full of fraud.

Slow Down Music - Where I commit thought crimes...

Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

Renegade

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Re: Peer Review and the Scientific Process
« Reply #127 on: February 08, 2015, 05:06:13 PM »
Just saw this:



Slow Down Music - Where I commit thought crimes...

Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

Renegade

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Re: Peer Review and the Scientific Process
« Reply #128 on: February 08, 2015, 09:13:40 PM »
(Cross-post from down "there".)

And more from the fraud dept...

http://www.telegraph...ce-scandal-ever.html

Quote
Following my last article, Homewood checked a swathe of other South American weather stations around the original three. In each case he found the same suspicious one-way “adjustments”. First these were made by the US government’s Global Historical Climate Network (GHCN). They were then amplified by two of the main official surface records, the Goddard Institute for Space Studies (Giss) and the National Climate Data Center (NCDC), which use the warming trends to estimate temperatures across the vast regions of the Earth where no measurements are taken. Yet these are the very records on which scientists and politicians rely for their belief in “global warming”.

Homewood has now turned his attention to the weather stations across much of the Arctic, between Canada (51 degrees W) and the heart of Siberia (87 degrees E). Again, in nearly every case, the same one-way adjustments have been made, to show warming up to 1 degree C or more higher than was indicated by the data that was actually recorded. This has surprised no one more than Traust Jonsson, who was long in charge of climate research for the Iceland met office (and with whom Homewood has been in touch). Jonsson was amazed to see how the new version completely “disappears” Iceland’s “sea ice years” around 1970, when a period of extreme cooling almost devastated his country’s economy.



Change all the data to make it fit your narrative, then let people review your narrative and verify it against the data.

Oh, where have we heard that story before? Oh... that's right... a Merck whistleblower...

Hm...
Slow Down Music - Where I commit thought crimes...

Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

40hz

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Re: Peer Review and the Scientific Process
« Reply #129 on: February 08, 2015, 09:18:18 PM »
^A thought: perhaps we're too easily equating 'corporate researchers' with scientists? And 'corporate sponsored research' with science? ;)

Renegade

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Re: Peer Review and the Scientific Process
« Reply #130 on: February 08, 2015, 10:30:33 PM »
^A thought: perhaps we're too easily equating 'corporate researchers' with scientists? And 'corporate sponsored research' with science? ;)

What's wrong with you? Are you one of those anti-vaxxers? :P ;)
Slow Down Music - Where I commit thought crimes...

Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

40hz

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Re: Peer Review and the Scientific Process
« Reply #131 on: February 09, 2015, 01:17:34 AM »
^Far from it. ;D ;)

Renegade

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Re: Peer Review and the Scientific Process
« Reply #132 on: February 09, 2015, 10:32:38 AM »
^Far from it. ;D ;)

So you believe in corporate research then? ;)

(You can't have it all and have it both ways...)

B-b-b-but...
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barney

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Re: Peer Review and the Scientific Process
« Reply #133 on: February 09, 2015, 10:37:08 AM »
(You can't have it all and have it both ways...)

Why not  :-\ :P???

40hz

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Re: Peer Review and the Scientific Process
« Reply #134 on: February 09, 2015, 10:55:59 AM »
@Ren - I don't.  :P

And there are far more options than the false dilemma/excluded middle fallacy you're introducing.

Because there's more than enough good solid science to support the benefits of vaccination that I don't need to rely on self-serving corporate studies; or the clueless rants of some ex-Playboy Playmate; or the sturm und drang of some fundamentalist preachers; or actor and cable gabfest host Bill Maher's snarky verbal gamesmanship to reach the conclusions I have regarding it.

Many who argue otherwise however...(see 0:45-0:58 in the "If Google Were a Guy" video below):



For the record, this (below) is where I stand on the "controversy." I'd use my own words, but Ms. kirkland cuts to the chase better - and quoting her requires less typing on my part  ;):

Quote
[They]have built an alternative world of internal legitimacy that mimics all the features of the mainstream research world — the journals, the conferences, the publications, the letters after the names — and some leaders have gained access to policy-making positions. Mixing an environmentally inflected critique of vaccination and Big Pharma with a libertarian individualist account of health has been a resonant formulation for some years now, with support flowing in from both the Left and the Right.

- Anna Kirkland in The Legitimacy of Vaccine Critics: What Is Left after the Autism Hypothesis? published in Journal of Health Politics, Policy and Law - October 2011.

It's not about taking sides, It's about getting the bottom of the matter as far as you can possibly get in the face of all the chaff whirling around most (mostly faux) scientific "controversy" these days. I also don't see the need to go through life with a siege mentality. I can be concerned about issues without reducing them to a verbal tennis match. At least most times.  (Hey! If you want a Mother Theresa - go see Mother Theresa! :P)
« Last Edit: February 09, 2015, 11:09:37 AM by 40hz »

40hz

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Re: Peer Review and the Scientific Process
« Reply #135 on: February 09, 2015, 11:28:43 AM »
Moving away from the science of vaccination, and over to the socio-political side of the debate, I found this article excerpt to be something to think about. It's by obstetrician gynecologist Dr. Amy Tuteur M.D. And the rest can be found on her blog The Skeptical OB.

Quote
What everyone gets wrong about anti-vaccine parents


We told them this would happen.

We told them that it was only a matter of time before a childhood disease that had nearly been eliminated from the US would come roaring back if they failed to vaccinate their children. And that’s precisely what has happened. Measles has come roaring back, but not simply because a child incubating measles visited Disneyland.

Twenty years ago, if the same child had visited Disneyland, the measles would have stopped with him or her. Everyone else was protected — not because everyone was vaccinated — but because of herd immunity. When a high enough proportion of the population is vaccinated, the disease simply can’t spread because the odds of one unvaccinated person coming in contact with another are very low.

Of course, we told them that. We patiently explained herd immunity, debunked claims of an association between vaccines and autism, demolished accusations of “toxins” in vaccines, but they didn’t listen. Why? Because we thought the problem was that anti-vax parents didn’t understand science. That’s undoubtedly true, but the anti-vax movement is NOT about science and never was.

The anti-vax movement has never been about children, and it hasn’t really been about vaccines. It’s about privileged parents and how they wish to view themselves.

1. Privilege

Nothing screams “privilege” louder than ostentatiously refusing something that those less privileged wish to have.

Each and every anti-vax parent is privileged in having easy and inexpensive access to life saving vaccines. It is the sine qua non of the anti-vax movement. In a world where the underprivileged may trudge miles to the nearest clinic, desperate to save their babies from infectious scourges, nothing communicates the unbelievable wealth, ease and selfishness of modern American life like refusing the very same vaccines.

2. Unreflective defiance of authority

There are countless societal ills that stem from the fact that previous generations were raised to unreflective acceptance of authority. It’s not hard to argue that unflective acceptance of authority, whether that authority is the government or industry, is a bad thing. BUT that doesn’t make the converse true. Unreflective defiance is really no different from unreflective acceptance. Oftentimes, the government, or industry, is right about a particular set of claims.

Experts in a particular topic, such as vaccines, really are experts. They really know things that the lay public does not. Moreover, it is not common to get a tremendous consensus among experts from different fields. Experts in immunology, pediatrics, public health and just about everything else you can think of have weighed in on the side of vaccines. Experts in immunology, pediatrics and public health give vaccines to their OWN children, rendering claims that they are engaged in a conspiracy to hide the dangers of vaccines to be nothing short of ludicrous.

Unfortunately, most anti-vax parents consider defiance of authority to be a source of pride, whether that defiance is objectively beneficial or not.

3. The need to feel “empowered”

This is what is comes down to for most anti-vax parents: it’s a source of self-esteem for them. In their minds, they have “educated” themselves. How do they know they are “educated”? Because they’ve chosen to disregard experts (who appear to them as authority figures) in favor of quacks and charlatans, whom they admire for their own defiance of authority. The combination of self-education and defiance of authority is viewed by anti-vax parents as an empowering form of rugged individualism, marking out their own superiority from those pathetic “sheeple” who aren’t self-educated and who follow authority...

I didn't see anything in any of the above that contradicted my observations and impressions when attempting to have a rational conversation with those who identified themselves as part of the anti-vax crowd. Their overwhelming sense of social privilege and innate mental (and moral) superiority was almost painful to witness. In many respects, those were their most defining traits.

Dr. Tuteur has a series of well-argued posts on the whole anti-vaxxer issue, all of which are well worth reading IMO. Go look. :Thmbsup:

tomos

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Re: Peer Review and the Scientific Process
« Reply #136 on: February 09, 2015, 12:39:46 PM »
Isn't this getting off-topic?
I will say:

1) I read an article lately that claimed that 92% of non-vaccination was due to poverty. It referenced this report:
Safety and adherence: Issues that hinder childhood vaccinations by Jamie Michelle Womack, PA-C
http://www.web.archi...accines0110_2845.pdf (PDF)
relevant quote:
Barriers to adherence
Although increasing in numbers, families who seek exemptions from vaccination are by far in
the minority. Among families who are not opposed to vaccination, adherence rates are influenced by factors related to both characteristics of the parent and child and the health
care system structure. Race, education, socioeconomic status, access to health care, family demographics, and attitudes towards health care all affect vaccination adherence rates.32,33 Among parents with concern about the safety of vaccines, 72% nonetheless vaccinated their child primarily because of the risk of their child getting the disease and 17% cited state laws for enrollment into school or daycare.34 In a large-scale study of parental health beliefs about the vaccination process, 74% of parents found nothing difficult about the process. Concern about
side effects was the most commonly reported barrier (22.6%) followed by concern over the number of immunizations required at a single visit, but these concerns did not impact immunization rates. One study concluded that only 8% of underimmunization is related to parental perception of the immunization process.


2) Re previous post: That's all well and good 40, but I *know* that vaccine implementation over the years has been very high-handed - the system (for want of a better term) has done itself no favours there. As me & Ren said already:

Tomos hits exactly what we should be concerned about:

(FWIW I'm broadly pro-vaccine myself, but dubious about the methods used to force it on the populace, and dubious about relations between the FDA and the corporations developing the vaccines.)

But, those issues are about 1) forced medication, and 2) corruption, which while a degree in philosophy or law is certainly an advantage in discussing them, there's enough wiggle room for input from others. :)

However, that's off topic.

3) I suggest starting a thread (in the basement would be a good bet) to discuss, but FWIW I really dont think it's worth persuing...
Tom
« Last Edit: February 09, 2015, 01:01:16 PM by tomos, Reason: added quote from article in spoiler »

40hz

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Re: Peer Review and the Scientific Process
« Reply #137 on: February 09, 2015, 12:50:18 PM »
3) I suggest starting a thread (in the basement would be a good bet) to discuss, but FWIW I really dont think it's worth persuing...

In the wake of of a comment like that I hardly feel like discussing this much more either. Later! :) :Thmbsup:

tomos

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Re: Peer Review and the Scientific Process
« Reply #138 on: February 09, 2015, 01:28:08 PM »
3) I suggest starting a thread (in the basement would be a good bet) to discuss, but FWIW I really dont think it's worth persuing...

In the wake of of a comment like that I hardly feel like discussing this much more either. Later! :) :Thmbsup:

just in case: I didnt mean that personally against you or your views. I just think it's a topic that's with a high probability going to end up in the basement anyways.

(A bit rich of me though, to make those points you quoted, just after having written about the topic myself...)
Tom

40hz

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Re: Peer Review and the Scientific Process
« Reply #139 on: February 09, 2015, 04:44:46 PM »
3) I suggest starting a thread (in the basement would be a good bet) to discuss, but FWIW I really dont think it's worth persuing...

In the wake of of a comment like that I hardly feel like discussing this much more either. Later! :) :Thmbsup:

just in case: I didnt mean that personally against you or your views. I just think it's a topic that's with a high probability going to end up in the basement anyways.

(A bit rich of me though, to make those points you quoted, just after having written about the topic myself...)

Ok. Since you were courteous enough to reply, I feel I should return the courtesy and respond back. :)

I'd like to suggest that in any thread alleging deliberate malfeasance, such that the validity of the scientific method along with the process of peer review are brought into question, you can't avoid a discussion of the people (on either side of the debate) behind it - or -  the motivations and agendas driving at least some of the debate.

This is not a scientific crisis. It's a people problem. So I can't really see where it's off-topic to raise questions about people's behaviors, or their unsupported assertions and arguments, as they relate to the larger issue. Nor do I see where doing so should automatically point the discussion towards the basement.

Sometimes the scientific quest for truth raises uncomfortable questions. And while some respect is due almost any position if it is well-considered and well intentioned, there's nothing that says such a discussion has to leave everyone feeling good by the end of it.

Scientific progress is often disruptive and uncomfortable. Few people enjoy having their most strongly held beliefs and understandings challenged or (even worse) proven conclusively wrong. The recent theories of the multiverse and dark matter have dumped half of established cosmology and physics into the dumpster leaving those working in the field scrambling to re-examine and re-test all their former understandings. Just as Einstein's theories did a generation earlier. And as did Fermi's, Pasteur's, Galleo's, and a very long list of other scientists stretching back to antiquity. Growth is often painful - and intellectual growth often doubly so.

And since science - and science reporting - is done by humans, you can't simply ignore the vagaries of human psychology, and it's often hidden agendas, when evaluating arguments against (and for) the process of scientific discovery and peer review.

Let's take a closer look at the so-called scandal surrounding temperature data...

Ars Technica had an interesting article recently that looks at the whole temperature data "controversy." They've come to the conclusion that not only is this NOT the "scandal" that the news media has been hyping - it's a rerun of a debunked accusation that was made a few years ago by Fox News. And at the bottom of it this time is a bona fide professional contrarian (and non-scientist) by the name of Christopher Booker.

Quote
...We knew this already; we knew it two years ago when Fox published its misguided piece. But our knowledge hasn't stopped Booker from writing two columns using hyped terms like "scandal" and claiming the public's being "tricked by flawed data on global warming.” All of this based on a few posts by a blogger who has gone around cherry picking a handful of temperature stations and claiming the adjustments have led to a warming bias.

Why would Booker latch on to this without first talking to someone with actual expertise in temperature records? A quick look at his Wikipedia entry shows that he has a lot of issues with science in general, claiming that things like asbestos and second-hand smoke are harmless, and arguing against evolution. So, this sort of immunity to well-established evidence seems to be a recurring theme in his writing...

Read the full Ars Article here.

superboyac

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Re: Peer Review and the Scientific Process
« Reply #140 on: February 09, 2015, 05:02:55 PM »
This may be off topic, but I wouldn't mind some of your input here.
Recently, a lot of people around me have been getting worked about about the anti-vaccination issues.  I've been listening to the arguments, and I must say that I'm legitimately confused.  Politics or beliefs aside, the question I want to answer is, "Should I vaccinate?  How do I make this decision wisely?"
The closest I've been able to come to an answer is along these lines:
Let's say there's a disease where I have 5% chance of dying.  The vaccine is available, and with it there is the 1% risk of dying.  So in that case, the gamble is mathematically worth the risk.

But it's just not that simple.  Do we know these percentages?  What if the vaccine is for a non-lethal disease, like a cold or mild flu?  Are these risk quantification reliable?  I don't know the answer at all, to be honest.  And it's a sensitive issue in my circles as there actually are cases of life-altering mental problems that have been attributed to vaccination.  I never ask, but I want to ask how do we know it was the vaccines? 

tomos

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Re: Peer Review and the Scientific Process
« Reply #141 on: February 09, 2015, 05:16:04 PM »
So I can't really see where it's off-topic to raise questions about people's behaviors, or their unsupported assertions and arguments, as they relate to the larger issue. Nor do I see where doing so should automatically point the discussion towards the basement.

good points :up:
Tom

40hz

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Re: Peer Review and the Scientific Process
« Reply #142 on: February 09, 2015, 07:47:56 PM »
@superboyac - In the interests of not derailing this thread, I sent you a PM with my input.  8) :Thmbsup:

IainB

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Put a sock in it.
« Reply #143 on: February 09, 2015, 10:36:06 PM »
Just to be pedantic: a good deal of the foregoing comments over the last day or so seem to be related to WHO (some pundit or other) said WHAT (POV or argument) about something scientific or pseudo-scientific. I could be wrong, of course, but in some of those comments, and in some of the linked articles, what seems to be important is proving one's position (bias) as being closer to the "truth" than someone else's position/bias.
That does not necessarily seem to be entirely relevant to adding to our understanding of Peer Review and the Scientific Process.

I would suggest that what is relevant is the observational data and results of experiments/trials and the falsifiability of those experiments/trials - be it wind speeds, global temps, numbers of infections/vaccinations, the incidence of caries in certain age groups, or something else.

For example, let's take a case in point - vaccination:
Let me comment on the vaccination issue, drawn from my own experience. Some years back, the then NZ Director of Public Health (Dr. Colin Tukuitonga) sponsored a new project to set up a NIR (National Immunisation Register) database, to record and track all candidates for vaccinations, and I (as an external consultant) was appointed as project manager to set it all up and initiate the project, and then hand over to a yet-to-be-selected project manager for the duration of the rest of the project lifecycle. This was a big and important project within the Ministry of Health and critical to the objective of the MoH for maintaining/improving the public health and especially that section of it called "children".
In setting up the project, I focussed initially on the solidity of the business case and an analysis of the potential risks of failure of this project.
The business case was straightforward and compelling: Children were dying needlessly. The project had been given some urgency due to the increasing incidence of then epidemic proportions of a disease called "Meningococcal B".  This dreadful disease was killing mostly children, and was preventable. Vaccination trials and programmes showed that vaccination had sharply reduced the incidence of the meningococcal disease in other developed countries, and so a vaccine for the prevalent strain in NZ (pathogen type "B") was developed and scheduled to fit in with the NIR development project.
The NIR database enabled the potential candidates (children) to be tracked and monitored to ensure that all children were vaccinated. The target population data was built from birth records and doctors' records of their family/child patients, and updated by doctors who recorded children as they moved (with their families/guardians) into other geographic practice areas and registered with new GPs there.

My involvement with the project finished after handover, but about 2 years later I bumped into the project sponsor whilst waiting in a bank queue. I asked him how the project had gone. He said with some exasperation that it had run about 8 months over its planned 18 months (I think it was) due largely to risks which eventuated - some of which I had predicted, but some of which I would not have been able to anticipate at the time. He added that it was now successfully vaccinating/covering all the at risk target population and the disease statistics were in rapid decline - so it was a success.

A few years later, I took my then 8 y/o daughter to an appointment at our local doctor's surgery for her to have her scheduled vaccinations. My daughter has an irrational fear of needles/vaccinations, and had been dreading this visit, but she kept a brave face on things.
As we were sitting in the waiting area, I noticed a magazine (I think it may have been "North & South"). The magazine had a striking picture on the front cover: it was a photo of a little smiling blond girl aged about 5, sat on a chair, but she had no arms or legs (they terminated in stumps at her elbows and knees). I read the article inside. Apparently, her parents had moved from one area to another shortly before what would have been her scheduled meningococcal B vaccination, but had not thought it important to get around to registering with their new local GP, so the child's current whereabouts was not on the NIR database. Had they been, then she would have had her meningococcal B vaccination on schedule, but instead she fell foul of the statistical risks and caught meningococcal B, and would have died had not the doctors amputated her limbs in order to save her life - meningococcal B causes progressive massive internal haemorrhage and destroys the body parts.

I showed the story to my daughter, and pointed out that this was exactly what I had been telling her - that vaccinations reduced the risk of her dying or being disabled by some horrible but preventable disease. The bad luck of the little blond girl was a sobering and very real thing. You can't fight the statistical odds.
Yet I am amazed at the number of times I have read of or heard people saying "I'm not having my child vaccinated. It's too dangerous - just look at such-and-such" or "Just look at what [insert name of anti-vaccination pundit] says about vaccination risks".

It reminds me of a case in the UK where a highly experienced police dog handler had 2 superbly trained Alsatian police dogs, which lived at his home as much-loved and trusted members of the family. One day, he was out of the house and his wife was in an upstairs room or something, and their 5 y/o daughter was playing downstairs in the kitchen, where the dogs were. When the mother came downstairs, she found that the dogs had killed the child.
A newspaper reported the father as saying later that he couldn't understand why the dogs had killed her - he was absolutely sure that they would be safe with the child - he would have "staked his life on it".
Well, of course, he didn't stake his life on it at all. He all-too-easily staked her life on it, and without even asking her if that was OK.
If parents had to suffer punishment with the direct consequences of their irrational decisions made on behalf of their innocent and trusting children, then they might think twice about such things. Or then again, maybe not (say) if they believed "it was God's will" or something equally idiotic, thus enabling them to sublimate the blame into something else. Anything but my fault, please God.

I imagine how the parents of that little girl pictured in the magazine must shudder at what they have done, seeing every day the needlessly hacked-up body of their beautiful little girl as she grows up. Try living with the consequences of that.
« Last Edit: February 10, 2015, 01:01:22 AM by IainB, Reason: Additional info for clarity. »

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Re: Peer Review and the Scientific Process
« Reply #144 on: February 10, 2015, 04:12:26 AM »
And there are far more options than the false dilemma/excluded middle fallacy you're introducing.

I was wondering if I'd get called out on that~! ;D  :tease:

It's by obstetrician gynecologist Dr. Amy Tuteur M.D. And the rest can be found on her blog The Skeptical OB.

Regarding the article there, it was a nicely done bit of name calling, and not much more.

The vax debate is pretty toxic. Nobody actually tries to communicate. It's nothing more than a yelling match with lots of name calling in the VAST majority of cases.

The most toxic people are the rabid pro-vaccine people that do their utmost to alienate the exact people whose behaviour they want to change. It's counter-productive at best. Then there's the crowd screaming for governments to make them mandatory... like that'd ever work out well...

This is not a scientific crisis. It's a people problem.

Yep. That.

Nor do I see where doing so should automatically point the discussion towards the basement.

Because the topic is toxic. People are not even remotely rational about it. It would degenerate quickly.

Now, a discussion about the discussion, that can probably be had much more sanely.

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Re: Peer Review and the Scientific Process
« Reply #145 on: February 10, 2015, 04:38:24 AM »
This may be off topic, but I wouldn't mind some of your input here.
Recently, a lot of people around me have been getting worked about about the anti-vaccination issues.  I've been listening to the arguments, and I must say that I'm legitimately confused.  Politics or beliefs aside, the question I want to answer is, "Should I vaccinate?  How do I make this decision wisely?"

If you consult with a doctor that isn't blindly religious on the issue, most likely your doctor will recommend vaccination, but not necessarily for everything. Not all people need all vaccines. There actually is room for thought on the topic, though the current dialectic pretty much excludes any rational debate.

For example, do you need to be vaccinated for Japanese encephalitis? It's a horrible, crippling disease that utterly destroys people. Chances are that you don't as it is only found in certain places.

Are you at risk for cervical cancer? If you're male, then no. And here is where the insanity begins, because there are quite a few people that want forced vaccinations for boys. I.am.not.kidding.

Talk to 1 or more doctors. Read up on the issues.


The closest I've been able to come to an answer is along these lines:
Let's say there's a disease where I have 5% chance of dying.  The vaccine is available, and with it there is the 1% risk of dying.  So in that case, the gamble is mathematically worth the risk.

That's correct given that you will get the disease. If there's a 1% chance of contracting the disease, then 5% * 1% vs. 1% doesn't justify the vaccine, mathematically that is. But that doesn't take into account other possible problems from the disease, e.g. 50% chance of blindness, etc.

All too often people talk about mortality rates, but blindness, deafness, and many other horrible effects also come with some diseases.

Then there are diseases like rubella that aren't serious (or as serious as others). Rubella is mostly relevant for pregnant women.

But it's just not that simple.  Do we know these percentages?  What if the vaccine is for a non-lethal disease, like a cold or mild flu?  Are these risk quantification reliable?  I don't know the answer at all, to be honest.  And it's a sensitive issue in my circles as there actually are cases of life-altering mental problems that have been attributed to vaccination.  I never ask, but I want to ask how do we know it was the vaccines? 

How do we know? Good question. When you look at some of the crippling effects in some cases, and the timelines, then it's pretty obvious, but that's not scientific proof, though it is sometimes enough to get settlements from the secret vaccine courts.

When a friend of mine gets a flu shot, he's pretty much guaranteed to get the flu -- and he no longer gets any flu shots. But, that's annecdotal.

I think it really depends on the person - not all people are the same.

Oh, I just remembered a bit more insanity... This is fun~! ;D

A common argument that I read all the time is about "the children" and how people want to exclude unvaccinated kids from schools.

Ok. For the sake of argument... Let's run with that. ;)

Some vaccines turn the recipient into a carrier for anywhere from 2 weeks to 90 days.

So, for those vaccines, shouldn't vaccinated children be excluded from schools until they are no longer contagious? Not all kids can get the same vaccine at the same time (if that even mattered).

In the first bit above, we have no evidence that any unvaccinated child has any disease, but in the second instance, we have clear evidence that the child is contagious. What to do? :P

Fun fun fun~! ;D

I do like to pick on the pro-vaccine crowd as they're such wonderful targets, and especially the sanctimonious, uneducated ones that merely parrot what they heard on CNN. Picking on the anti-vaccine crowd isn't really much fun. Like, how do you make fun of a kid getting measles, which has a 0.1% mortality rate in developed countries? There really isn't much of a joke there.

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40hz

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Re: Peer Review and the Scientific Process
« Reply #146 on: February 10, 2015, 08:35:19 AM »
Information on the different types of vaccines can be found here. Approaches being considered for future vaccines can be found here.

@Ren - IIUC you can't (except in that rare situation with the old oral polio vaccine - which is no longer administered) come down with the illness that an attenuated-live vaccine is designed to provide immunization for unless the batch that was administered was defective. And my understanding is that cases of defective vaccine batches making it into actual circulation are extremely rare occurrences.


Some vaccines, however, do lower your overall immune response such that you're more susceptible to an opportunistic infection while your body is generating the immuno response to the pathogen in the vaccine. So I'm guessing your friend may be getting sick after being vaccinated for flu because his immune system doesn't respond well to vaccination, and either takes a bigger hit, or takes longer than usual to recover from one. If so, during that period he's more open to infection by any one of the thousands of other flu strains in the environment that the "annual" flu vaccine (which only covers a small number of the most anticipated strains) is engineered to help you deal with.

That's why some people who come down with a serious flu infection also wind up with a case of "shingles" or pneumonia during their illness or recovery. (Happened to me once.) Which is why they're also starting to recommend people in certain age brackets be vaccinated (or re-vaccinated) for chickenpox/shingles along with pneumonia.

However, the real benefit of vaccination is realized when most of the population is immunized because vaccines go a long way towards reducing the disease's vectors of transmission. If one person contracts in a group of immunized people, the disease doesn't spread. Possibly a few others (including those vaccinated) will become infected. But that's about as far as it will go.

If a large portion of the population is not vaccinated however, and isn't already immune from a previous brush with that infection, you have the very real potential for another Disney scenario. The deadly consequences of uncontrolled contagion are such that even in the world of military planning, germ warfare is almost automatically ruled out as an option . And it's not due to any sense of showing decency towards a real or imagined enemy. It's done mainly out of a sense of "enlightened self-interest." And the military also routinely vaccinates troops "just in case."

When professional mayhem creators such as the military acknowledge the dangers of contagion enough to rule it out as a weapon system, and vaccinate their own as a precaution based on established knowledge of how disease propagates and spreads, I find it interesting that so many people (who pride themselves on their self-'education') - and who benefited from vaccination themselves while growing up - are so convinced of the inefficacy and "danger" of vaccines. And with so little solid evidence to support their belief. Indeed, there's a huge amount of rock solid scientific evidence that clearly and directly contradicts the anti-vaccination argument. And now they're so convinced that their Googled "instant expertise" exceeds that of the genuine professionals in the field that they're even willing to put their own (and other's) kid's health (and lives) on the line to prove they're right. That just boggles my mind. Small wonder they had to drag that old brickbat "Conspiracy!" and toss some ad hominem attacks into the discussion to 'support' their position.

But it is true that vaccines are not a panacea for every individual. And they may harm a minuscule portion of the population despite all the precautions taken to assure their safety. There will always be boundary conditions and exceptions in biology. And risk will always be present with any vaccine or medication, no matter how slight.

FWIW my doctors have always advised me to avoid crowds and take it easy for a day or two after I've gotten a vaccination so my system has time to adjust. Vaccines aren't one of those simple "dose & go" or "magic bullet" solutions like antibiotics often are. They don't kill or ameliorate an infection themselves. They "encourage" your body develop its own defense against them. Which takes your body time to fully boot up.

Like most things in medicine, it seems like it's seldom "just one simple thing," but rather a combination of factors on different levels of an individual's health regime (i.e. locale, environment, genetics & gender, age, diet & nutrition, exercise, competent medical care and advice, drugs, vaccines, timing, etc.) that yields the most benefit.

I've been given to understand that vaccines (by themselves) aren't a magic cure-all. But I haven't heard immunologists or competent medical doctors claim they are either. Vaccines are, however, damn good insurance. With vaccines it's all about risk minimization and mitigation. Because at this stage of our medical knowledge and technology, that's about as good as we can make it.

« Last Edit: February 10, 2015, 11:04:29 AM by 40hz »

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Re: Peer Review and the Scientific Process
« Reply #147 on: February 10, 2015, 10:30:34 AM »
@Ren - IIUC you can't (except in that rare situation with the old oral polio vaccine - which is no longer administered) come down with the illness that an attenuated-live vaccine is designed to provide immunization for unless the batch that was administered was defective. And my understanding is that cases of defective vaccine batches making it into actual circulation are extremely rare occurrences.

Sorry, but no. There are some vaccines that make the patient contagious for a period of time. You only need to check the insert to verify.

You can find it in some inserts under some section  like in the below, 5.8 "Risk of Vaccine Virus Transmission". Here's a bit for the VARIVAX vaccine:

Screenshot - 2015_02_11 , 3_08_28 AM.png

There are more. That's just one. The recommendation is for 6 weeks.

Here's a bit from another insert:

Screenshot - 2015_02_11 , 3_18_32 AM.png

That lists 28 weeks, or 7 months.

Again... just what part of this is hard to understand for people? Everyone wants to believe that vaccines are some sort of magical pixie dust.

PUBLIC SERVICE ANNOUNCEMENT (PSA):

VACCINES ARE NOT MAGICAL PIXIE DUST!

Vaccines are, however, damn good insurance. With vaccines it's all about risk minimization and mitigation. Because at this stage of our medical knowledge and technology, that's about as good as we can make it.

Yes. Exactly.

But the pro-vaccine crowd almost ALWAYS touts all the positive benefits and completely ignores any of the possible adverse issues or other "inconvenient" facts. Again... this is about approaching the topic sanely and measuring benefits vs. costs.

I'm sorry, but nobody gets to choose what parts of reality apply to them. Unfortunately, 100% of reality applies to everyone... vaccine advocates included.

This only goes to show, yet once again, how the mainstream views are so grossly distorted and perverse.

What really pisses me off is all these self-righteous zealots who preach "science" and then want to ignore anything that doesn't fit their personally acceptable narrative. This is a recurring theme in many fields, not just in "vaccines".

Gravity applies to Wile E. Coyote just as it does to everyone else. Nobody escapes nature. Not even psychotic zealots. :P

Now, chickenpox (for the Varivax vaccine above) isn't very serious. But it's just one example. Not all vaccines are equal, and the zealots trying to portray them as all being unicorn farting rainbows do nothing to help the situation.

Each vaccine needs to be treated on its own merits. Period. End of story. Most offer great benefits, but lying about them does not engender trust.

Given the massive disinformation and the non-stop lies about vaccines, can we blame people for being against them?

Or, would you trust someone that you knew constantly lied to you?

This isn't difficult to understand -- the vaccine zealots do more harm than good when they constantly lie and cover up inconvenient facts time and time again.






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40hz

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Re: Peer Review and the Scientific Process
« Reply #148 on: February 10, 2015, 11:22:01 AM »
Ok. I stand corrected. But that's also VARIVAX. (Chicken-pox, right?) So how many more vaccines have similiar concerns precisely? Current anti-vax arguments say all vaccines are unacceptably dangerous. I don't think that's correct.  (BTW, chicken pox is a very serious illness if contracted by an elderly person or someone with severe respiratory health problems.)

Going back to the the chance of spreading something post vaccination - if people who are exposed are already immunized either from a previous bout with the actual disease - or have been previously vaccinated as most vaccine protocols recommend - the individual infection is extremely unlikely to spread to those exposed.

Again, they're citing a boundary situation that could possibly become an issue if only a few people are vaccinated - and the majority of the population are not. If 99% of the population is already immune, the occasional person who may become contagious post-vaccination does not pose a serious risk to the general population. Just the holdouts

Exceptions can be given till the cows come home. I think it's more beneficial to focus on the norm as long as those exceptions remain exactly that - statistically insignificant.

Just my :two: anyway. The demand for perfection remains a barricade to accomplishing demonstrable good - if you allow it. :)

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Re: Peer Review and the Scientific Process
« Reply #149 on: February 10, 2015, 02:23:36 PM »
I would suggest that what is relevant is the observational data and results of experiments/trials and the falsifiability of those experiments/trials - be it wind speeds, global temps, numbers of infections/vaccinations, the incidence of caries in certain age groups, or something else.

This times infinity.

I hadn't been paying attention to this discussion for a while, and I'm going to wait to add my specific thoughts on a couple of the specific topics until I have time to write. And yes, that means walls of text, so I apologize in advance.

I did, however, want to highlight what IainB posted because he managed to summarize the entire issue in as succinct a manner as possible. For a much wordier treatise along the same lines, I highly recommend the transcript of a lecture Michael Crichton gave at Cal Tech shortly before his death.

Aliens Cause Global Warming
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Before they beat me bloody down at the station
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I got a billion years probation
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I recommend reading through my Bio before responding to any of my posts. It could save both of us a lot of time and frustration.