It’s hard to imagine a chunk of land that, apparently, once rivalled the Himalayas in height crunching into and pushing it’s way under New Zealand. (If you want to skip the introduction, jump to about four and a half minutes into the video.)

Click here to view the embedded video.

As a bonus, here’s a map of the earthquakes at Christchurch to date,

More at Code for life:

Crick’s letter to son, aged 12, explaining DNA structure model

Sea stars and mosaics

Dear journalists and editors, (again)

It’s a small, small world (and three wise monkeys)

One example of why all those genomes from different species are useful to biologists

When things grow wild – post-earthquake natural succession in Christchurch gardens

More details and the booking form (click the large blue ‘Register now’ button) are available on the Royal Society of New Zealand website.

His first talk was yesterday,*** but the last four talks are to be held over May 16th – May 23rd.

He’ll be promoting his new book, Sentinel Chickens. (You may be able to pick a copy up from the events – ?)

He’s the author of several other books including The Beginner’s Guide To Winning The Nobel Prize: A Life In Science and Pandemics: What Everyone Needs to Know. (He also advocated Seth Mnookin‘s book The Panic Virus® that I’ve previously reviewed.)

We’ve often written about vaccines here at sciblogs. Recently Helen Pertousis-Harris’, head of Auckland University’s Immunisation Advisory Centre has joined us with her blog, Diplomatic Immunity. A recent post by Siouxsie Wiles looks at the coronavirus originates from Saudi Arabia that epidemiologists and virologists are keeping an eye on. A few of mine are listed below.

Footnotes

* Including the dangerous-to-humans Ebola and Hendra viruses.

** Note there appear to be two talks at Dunedin, May 20th and May 21st.

*** This is the first notice I’ve had of the lecture tour, too.

Other articles on Code for life (further reading can be found in the links at the end of these articles):

Immunisation then and now

Vaccination – why learn the hard way?

Are too many vaccines too soon harmful?

Vaccination rates in NZ and what do those that delay infant immunisation think?

Thoughts on, and for, those trying to choose to vaccinate or not

Fact or fallacy, a survey of immunisation statements in the print media

Readers could try the winners of the inaugural Science Seeker Awards. Don’t ask me how 3 judges whittle down over 350 entries to a bit over a dozen winners. You can browse the full list of nominations too. Go for it. Good reading for free!

Some of my older writing is under my Writing page. (Another thing long due for an update or, realistically, more content for it.)

One reason I’m deferring is I’d write something grumpy about bioinformatics software development and the projects that generate them, featuring loud whinges like:

• PIs for goodness sakes insist the student test their code. Really test it. It’s really embarrassing to find one after another solution for a fairly straight-forward task isn’t up to real-world use. Embarrassing to think I’m part of the same field, that is. (And a bit depressing, too.) Note that’s not just bugs, but utility, which leads me to…
• If you’re going to have someone develop a method, insist they have some real-world project using it so they get to use what they make ‘for real’. I’ve touched on this topic before in Developing bioinformatics methods: by who and how. The developer might then have a hope of seeing what’s need to really use what they’re making. (It also works the other way around, that they understand what needs to be solved.)
• A project is not complete until it’s been properly documented. Properly is not a sketchy outline reminder to the author how they did it. It certainly is not failing to point out hidden assumptions in the code, limitations such as it bailing out on some types of input, etc., etc.
• And, er, on I could go…

But you’d be better to look to happier reading, eh? Check out the Science Seeker Award winning entries. (I don’t have time to – ha!)

Well, it seems we shouldn’t listen to you – that’s for certain!

You are getting basics wrong.

Let’s start with your analogy that, “The best-ever scientific knowledge was Newtonian mechanics. And Einstein blew it to bits.”

That is incorrect.

If you can’t get right something that simple, that well understood, why should we expect anything you say on climate science to be right?

Einstein’s work did not ‘blow Newtonian mechanics to bits’. The latter is very widely used, very usefully. Einstein’s work relates to conditions outside of the sorts of speeds, time-frames and distances that are typical of our daily lives.

You’ll see Newtonian mechanics used by engineers and scientists everywhere. It’s perfectly good for that. In fact, Einstein’s alternatives are inappropriate and needlessly complex for most applications.

Heck even simulations of macromolecules, something I have some familiarity with, uses Newtonian mechanics. It’s not ‘perfect’, but it is science; it’s pragmatic, used, and gets useful results.

You do realise that in writing “That’s incontrovertible” you are presenting certitude, the very thing you claim to oppose?

You also get wrong a very important basic. You offer that people should not listen to groups, implying that members of groups are ‘speaking in concert’. What you don’t say is that’s not the case for science. In science the consensus is the consequence of criticism of each other’s findings. Scientists don’t ‘toe lines’ the way members of political parties are obliged to!

Footnotes

See also Ken’s take on the climate science aspects.

* I have no idea how long moderation typically takes, if comments are usually accepted immediately or not, or who moderates the comments there. There no message given that the comment is in moderation or whatnot. I’m too busy to do more than quickly put this up here. Now, back to work… (A pity on such a lovely autumn day…)

Other possibly-related articles on Code for life:

Woo-ful MPs

Those behind charter schools are to be exempt from public scrutiny – ?

Paul Nurse on ‘anti-science doubters’ and the blogosphere

Elections – time for policies to be deposited in advance?

Why (some) people don’t trust science

You can change the ideas, but not the data

Communicating complex and post-normal science to the policy maker and the public — lessons from New Zealand

Here’s how to install a StatCounter visit counter into WordPress blogrolls. Or at least sciblogs blogrolls! – this is mostly for my blogging colleagues, but I hope those with other blogs should be able to follow along. In future posts I’ll describe adding a Sitemeter visit counter or a ClustrMap, which tracks where in the world those who visit your blog are from.

It’s fun to see how your blog is going, to keep tabs on if it’s suddenly getting a lot of visitors and where your visitors are from. The three main tools for tracking visitor statistics (more than just how many visit) are Sitemeter, StatCounter and Google Analytics.*

I recommend people use StatCounter over Sitemeter, owing to the latter’s erratic failures over the past year or so. (An on-going issue that seems to be, well, on-going.)

My description is particularly for where the bloggers don’t have access to the backend to install plugins, like sciblogs.

1. Sign up and start your tracking project

StatCounter offers a page-by-page, step-by-step process. It’s friendly, but has more steps.

Go to statcounter.com and click on ‘Sign up’ from their tabs, then enter the details. (You might like to use the name of your blog as the username. It‘s not a bad idea to get a gmail account dedicated to your blog.)

After clicking ‘Create Account’ on the bottom-right you’ll be presented with a page asking you to set up your first project:

(Sciblogs bloggers will want to use the full URL to their blog, e.g. http:sciblogs.co.nz/code-for-life/ for Code for life.)

When you enter the URL for your blog, you’ll see that StatCounter offers a title for the project, filling in that part of the form for you.

(Continuing down the left column of options, if New Zealand bloggers want to be added to Ken Perrott’s NZ blog rankings, you’ll want to check ‘Make Statistics Public’. You can leave the link to display alone as we’re going to set one up.)

If you’ve already been blogging for a while and are shifting from another visit counter, click on ‘Customize!’ immediately under the ‘Visible Counter’ option to the right. A pop-up will appear: if you click click on ‘Starting Count’ under the menu in the pop-up you can set how many visits you’ve already had. (No cheating!)

I suggest weekly emailed reports (the default).

You can either have the live counter in your blogroll and everyone will see how many visitors you’ve had right from your blog.

That’s the default setting – ‘Visible Counter’, to the right of the options.

You can also choose one of several images, what I’ve done for Code for life. To do that, check ‘StatCounter Button’, then select which image you like.

While you can have no image show, I suggest you display something or you’ll end up with an odd-looking gap in your blogroll.

Click ‘Add Project’ at the bottom-right.

2. Getting the web address to add to your blogroll

(I’m going to speed up a little here: if you want more screen shots, let me know.)

You should now be viewing a page titled ‘Choose an Installation Guide for your Website’: click on WordPress from the long list of guides.

You’ll now be asked which WordPress! We want WordPress.org, the second option: click on ‘Go to the open source WordPress.org installation guide’.

You’ll now be shown a page telling you how to enter their default code snippet. As we’re trying to install into the blogroll we get to do it a bit differently to these instructions.

Instead click on the link ‘install the plugin manually’ near the top of the page.

On this page you’ll see a complicated bit of code under the heading ‘Standard’. Click on the tab ‘Basic’. You should see something like this:

This is the web address we want to install into our blogroll. You’ll find that it’ll try select all of the code – copy all of it into a word processor or text editor and copy the piece we need. Select and copy the web address inside the src=”http://c.statcounter.com/8928698/0/4ee56701/0/” part, as I’ve boxed below. Leave the StatCounter page open in a browser tab – we’ll be coming back to it.

3. Installing the web address into your blogroll

Login to your WordPress Dashboard, and select ‘Links’ from the left column. Click ‘Add new’ near the top of the page. You should see a form to enter, with a series of entries (don’t forget the last one):

• Name – this is the name that shows on the Dashboard presentation of what links you have added, not what is shown on the page. I use ‘Stat Counter’.
• Web Address – here you want to enter the web address we copied from the StatCounter code.
• Description – I just use the same as for the Name field: ‘Stat Counter’, but you could write, say, ‘Hey! I’m really popular’ or whatever… :-) Users of your blog will see this if they roll their mouse over the StatCounter link.
• Categories – leave this set to ‘Blogroll’.
• Target – leave this set as _none. (Altering this takes control of what tab or page the link opens in, which is bad practice in my opinion – users can easily ask for it to be in another tab themselves if that’s what they want.)
• Link Relationship – I guess I can leave that up to your imagination…
• Advanced – This one is important. It must contain the web address we copied from the Stat Counter code.

Click ‘Add link’ (blue button to the right-top of the page) and check your blog. You ought to now have a link to StatCounter.

4. Finishing off with StatCounter

Go back to the StatCounter tab.

You should be on the ‘Default Guide’ page with the code snippet under ‘Basic’ that you copied. Go back one page from to the ‘Insert Code Snippet’ page. (Use the browser’s back button.)

Try clicking on the ‘Check Installation’ button on the right toward the bottom of the page. StatCounter will visit your blog and try work out if the StatCounter link has been set up OK.

You’ll probably get a message saying that you’ve only got a basic setup. That’s OK. That’s what we get for installing just the web address into the blogroll rather than the full plugin.

Once that’s done, you’ll get to go to your projects page.

I’ll leave you to the rest – it ought to easy enough to follow. Click on the project link, to the right of the little graph icons and you can tinker with your settings and explore the different statistics. (You’ll note some you can’t get, too.) Feel free to ask in the comments if you get stuck.

Footnotes

* I’m not going to cover Google Analytics, which works differently. For those that do look at this, countries may have country-specific Google Analytics sites, e.g. google.co.nz/analytics/.

Other tips on Code for life:

Reading winmail.dat files sent to Apple Mac users

Mac OS X — quickly inspecting the contents of a file

LyX for free word-processing

Skim – free PDF viewer and annotator for Mac OS

WWW database servers on Mac OS X 10.6.x, part I: Installing MySQL

I’d like to quickly highlight a few items not in the science challenges, as noted in the Report of the National Science Challenges (PDF file) under section 12: Other points the Panel wishes to bring to Government’s attention.

There were many examples amongst the submissions where the real deficit was not the absence of knowledge but the absence of its application. This was true for example in relationship to addressing issues of fresh water but it was also true in many other domains, particularly those where public policy settings were involved.

[My emphasis added.]

A desire to see more use of evidence in policy formation is something I’ve seen widely remarked on – and not just from the science sector.* I’d certainly like to see more of this myself.

ThePanel noted that for the Challenges to be successful there would be the need to ensure scientific excellence and that would require organisational structures similar to MBIE funded Platforms and TEC funded Centres of Research Excellence.

To my reading, this might suggest that organisation is intended to be based around the broad aims (as with the CoREs), rather than direct to tightly-focused projects (as with the ‘traditional’ grant-funding agencies). Some have remarked that the challenges look to be largely ‘business as usual’. Reading this I wonder if it will prove to be perhaps familiar broad research areas, but with the new funding channelled through a different organisational approach that reflects a focus on the larger objectives.

The Panel was concerned by the lack of significant proposals in educational research.

Those in education will appreciate this point. Alison Campbell** has written on this from time to time.

Elsewhere there is mention of leadership and communication issues. That last, I imagine, will catch the eye of those in science communication circles.

There’s also a hilarious typing typing error in section 12,

[…] if we are to advance on several fronts, not the least in suing the biological and physical sciences to greatest effect […]

A-hem…

I don’t mean to take away from what are in the challenges, but draw attention to that the report says there is more than what are in the challenges to be done,

[…] the mere fact that so many gaps exist suggests that there is a lack of strategic oversight in mapping our science and research capacities to national need.

If you think other things were not present in the funded challenges that deserve attention, feel free to tell people in the comments.

Footnotes

* Ben Goldacre takes this further to randomly controlled trials of policy. I’ve (briefly) touched on the general topic of evidence in policy in some earlier posts (e.g. Communicating complex and post-normal science to the policy maker and the public — lessons from New Zealand,  Elections – time for policies to be deposited in advance? and  What do scientists want from politicians?).

** Marcus Wilson and Michael Edmonds come to mind as others at sciblogs who likely have written the odd article on the topic.

Other posts at Code for life:

Social media for scientists

Ag Science hub to form near Christchurch, New Zealand

More inclusive re-entry to encourage departure to businesses?

Nature’s reproducibility effort: when to get data specialists on board

François Jacob

Publish a ‘popular science’ version of your thesis?

A large agricultural science hub based on AgResearch has been announced to be established near Lincoln University, a few kilometres from Christchurch.

AgResearch is New Zealand‘s largest non-University scientific research organisation, based in a number of centres throughout the country, including Palmerston North and near Dunedin (Invermay). Lincoln University is an agriculture-focused university near to Christchurch, the scene of large earthquakes in September 2010, February 2011 and through 2011.

Press releases (2 links) sketch an outline the aims (from the first, introductory passages and most of the generalised ‘nice noises’ (!) omitted),

AgResearch is planning to invest $100 million in facilities and resources over the next four years to boost scientific support for what is New Zealand’s largest economic sector and most important industry.

“This represents the largest investment programme focused on agricultural science in AgResearch’s history and will better position us to help the pastoral sector sustainably improve productivity, export performance and deliver greater value to the New Zealand economy,” says AgResearch Chairman Sam Robinson.

[…]

“We are proposing to have a focus on farm systems, environmental science and dairying at our Ruakura campus in Hamilton. Much of the beyond-the-farm-gate science is proposed to be at our Grasslands campus in Palmerston North. At Lincoln we are proposing to concentrate many of our on-farm research areas and our Invermay campus, near Dunedin, is proposed to predominantly focus on environmental and farm systems capability,” says Dr Richardson.

He says now that the programme has the support of shareholding Ministers, work will commence with a detailed design and consultation phase.

“Our first priority is working through the programme in detail with our staff. We will also be working with our scientific collaborators and sector partners to progress this investment.”

The new investment programme, starting this year, will be funded predominantly through the disposal of existing under-utilised assets, and will not require any new Government investment to be provided.

There are few additional details from current media reports, the main ones being that it is anticipated that around 900 staff will work at the hub, that the proposal was “put to the government by five partner organisations – AgResearch, DairyNZ, Landcare Research, Lincoln University and Plant and Food Research” and that the construction of the hub is targeted to begin in 2014.

Reports point to the hub being partly due to Lincoln University needing to rebuild it’s science facilities after the earthquakes.

Without meaning to play on any fears, I wonder if the phrase “will be funded predominantly through the disposal of existing under-utilised assets” will concern some. It might be read as trying to put a favourable spin on shutting some things down.

Much will await detailed plans and the time-frames they anticipate, and the extent they intend to move staff and research projects.*

Thoughts welcome in the comments below.

Footnotes

Initial comment from DairyNZ is also available.

* Shifting experimental work can be a major effort. (By contrast, my own line of work—computational biology—can readily be moved on fairly short notice and can be done from pretty much anywhere with good internet access.)

Update

I found on the Beehive website a PDF file of the concept drawing for the hub. If you want details, you’re best to explore the PDF, as you can zoom in, but I’ve placed a few image below to give readers some idea of the layout. This will, naturally, make more sense to locals or people who have visited Lincoln. The bottom left is Lincoln University. To the top-right is the Plant and Food campus. To the right of Lincoln University is the township centre. The green line is a cycle path. You’ll note there is ‘medium density housing’ planned as part of the hub (between the academic core part and the supermarket). I may add more images later, but readers are best to view the PDF if they wish to explore.

I’ve zoomed into the central part of the hub here:

Other articles on Code for life:

Crown Research Institute merger calls

Another R&D stimulation package leaves out the smaller players?

More inclusive re-entry to encourage departure to businesses?

Elections – time for policies to be deposited in advance?

Social media for scientists

A recent study addresses specifically this question.

Things that trigger an immune response are called antigens.

To compare how much “stuff” in vaccines you gave to different children, you want to compare the number of antigens you gave them.

Autism spectrum disorder is a neurological condition.

By comparing the number of vaccine antigens given to children with if they had autism or not, you can ask if the number of vaccine antigens affected the neurological condition of the children. (At least for autism.)

Autism spectrum disorders become apparent when the child is around 2-3 years old, so vaccines given up to two years of age where studied.

The researchers used data gathered during a previous study, using data from 256 children with ASD and 752 matched controls.

Two main different types of comparisons were made:

1. The total number of antigens from vaccines given up to either of 3 months, 7 months or two years old
2. The largest number of antigens given in any one day

They found that children that received different numbers of vaccine antigens all had the same chance of getting autism – the number of antigens the child received from their vaccines did not make a difference to the chance the child would develop autism.

This applied whether to both the total number of antigens from vaccinations up to two years old, or to the largest number of antigens given in one day. Similar results were found whether the child had ASD (autism spectrum disorder), autistic disorder or ASD with regression.

The authors put it a little more formally,

We found no evidence indicating an association between exposure to antibody-stimulating proteins and polysaccharides contained in vaccines during the first 2 years of life and the risk of acquiring ASD, AD, or ASD with regression. We also detected no associations when exposures were evaluated as cumulative exposure from birth to 3 months, from birth to 7 months, or from birth to 2 years, or as maximum exposure on a single day during those 3 time periods. These results indicate that parental concerns that their children are receiving too many vaccines in the first 2 years of life or too many vaccines at a single doctor visit are not supported in terms of an increased risk of autism.

The justification for this paper is mainly to offer straight-forward evidence that might address parents’ concerns,

A recent survey found that parents’ top vaccine-related concerns included administration of too many vaccines during the first 2 years of life, administration of too many vaccines in a single doctor visit, and a possible link between vaccines and learning disabilities, such as autism. All of the foregoing concerns were reported by 30%-36% of all survey respondents, and were reported by 55%-90% of parents who indicated that their children would receive some, but not all, of the vaccines on the recommended schedule.

A New Zealand study found similar concerns were held by some parents.

For scientists working in a particular area it’s common to draw many small pieces of evidence together to form to a conclusion. Scientists are used to working with little details and putting them together. That’s how biologists thought it very unlikely that vaccines would be linked to autism before the many studies^[3] (two links) that have found that vaccines are not linked to autism.

It’s a bit of a pain for anyone else wanting to know what the deal is, though — even for scientists who work in other areas of biology. And certainly a collection of many small points doesn’t fare well on the ’Web. Hopefully this simpler study will help address parents’ concerns.

This study is retrospective, looking at how things went. It complements tests done prior to licensing a vaccine for a schedule as our new immunisation blogger, Dr. Helen Petousis-Harris, tells us in her first blog post at sciblogs,

All infant vaccines are assessed for concomitant administration. This is a requirement for licensure if they are to be added to a schedule.

Visit her blog, Diplomatic Immunity, and welcome her to sciblogs.^[4]

Those that prefer videos, can hear Paul Offit speak on this at the MedScape website.

A brief aside on autism

Personally, I’d like to see the focus on autism be on tracking down causes, rather than convincing people of things most scientists consider well-established.^[5] I know I’m not alone in saying that. The authors briefly summarised the likely causes of autism (their citations removed for clarity),

The possibility that immunologic stimulation from vaccines during the first 1-2 years of life could be related to the development of ASD is not well supported by the known neurobiology of ASD, which tends to be genetically determined with origins in prenatal development, although possible effects in early infancy cannot be ruled out completely. It can be argued that ASD with regression, in which children usually lose developmental skills during the second year of life, could be related to exposures in infancy, including vaccines; however, we found no association between exposure to antigens from vaccines during infancy and the development of ASD with regression.

The results in a little more detail

For those who would like to dig deeper, here’s start. (Those that don’t might want to skip to the end for further reading. Or check out Helen’s blog.)

The full paper is available on-line free (PDF file). A summary is also available (web page). Details on the case controls are in the paper; I won’t repeat them here.

The results are presented as adjusted odd-ratios (aORs). Simple odds ratios are the odds that a child a with one level of antigens from vaccination will have autism compared to a child with a different level of antigens from vaccination.

An odds ratio of 1.0 would mean that the two sets of children being compared have the same odds of having autism despite different levels of antigens from vaccines – indicating that different levels of antigens don’t change the odds of having autism later.

Similarly, an odds ratio significantly greater than 1.0 would suggest that a higher antigen level was associated with autism. Conversely, an odds ratio significantly less than 1.0 would suggest that a higher antigen level was associated with a lower incidence of autism.

Lets look at the statistics reported.^[6] Here are the two key summaries, Tables II and III from the paper:

You’ll see that the lowest level of antigens (first column of results) is set to be the reference (set to 1.0) to which the other levels (next two columns) are compared to. So the first results of the second column of data of Table III (immediately above) are a comparison of the odds of ASD in children who received 26-50 antigens up to 3 months of age compared in children who received -25 antigens up to 3 months of age. The average odds was 0.98, very nearly 1.0, with a 95% confidence interval of 0.47 to 2.08 (more on that in a moment).

That table is a bit hard to read, so let’s zoom in on the key columns:

Better?

For each there is a lowest value and a highest value, shown in brackets to the right of the average (boxed in the table below). These values are 95% confidence intervals – the range of odds values that would have a 95% probability that the ‘true’ odds ratio value would fall within.

The rightmost column show results for looking at the data as whole using “a 25-unit increase in vaccine antigen exposure, analyzed as a continuous variable”.

The paper reports adjusted odds ratios. Adjusted odds ratios (aORs) take into account things that might confuse (confound) the results. I’ve included the full list of these in the footnotes at the end of this article as the list is rather long.

An explanation of odds ratios, including adjusted odds ratios, can be found in the short, open-access, paper Explaining Odds Ratios by Magdalena Szumilas (M.Sc.). It has links to further reading for those who might be interested.

As you can see every comparison overlaps with one. In particular, the ‘continuous variable’ approach has values that cluster tightly around one. These results indicate there is no relationship between vaccine antigen exposure and autism (ASD, AD or ASD regression).^[6]

As David Gorski concludes you can quibble about details, as always,

Yes, there were limitations to DeStefano et al in that it was retrospective. In addition, as the authors discussed, not all antigens are equal in evoking an immune response. Some have more epitopes (areas on the antigen molecule that can trigger an immune response) than others, and the study didn’t weight the antigens for the intensity of the immune response that they evoke. Even so, the antigenic load has fallen dramatically, and this study is based on the vaccine schedule of the 1990s. Indeed, the authors note that the antigen load due to the vaccine schedule has fallen from several thousand in the late 1990s to an estimated 315 in 2012.

It’s very hard to do truly ‘clean’ work on subject matter that has many complex issues.

One issue is that the number of antigens in the whole-cell vaccines (pertussis, typhoid) is much more that the number of antigens that the other vaccines. As the authors noted the large number of antigens in the whole-cell vaccines meant the data had two peaks, one for the children that did not receive the whole-cell vaccines and another peak with a higher antigen exposure for those that did receive these vaccines. (There is a large jump from 1-69 antigens per vaccine to over 3000 antigens for the DTP and typhoid vaccines, as seen in Table I from the paper below.)

The continuous variable model (the rightmost column in Table II and III) avoids this as it looks at a 25 unit increase in antigens. Furthermore the authors did additional analysis on the number whole-cell pertussis vaccines received and found,

no statistically significant associations between number of whole-cell pertussis vaccine doses received between birth and age 2 years and any of the ASD outcomes; ORs (95% CI) for each increase of 1 whole-cell pertussis vaccine dose were 0.956 (0.793-1.152) for ASD, 0.989 (0.700-1.397) for AD, and 0.761 (0.380-1.525) for ASD with regression

There are, of course, other ways of looking at potential relationships between vaccines and autism. One is to look at the rate of autism in nations that elected to withdraw a vaccine, as Japan did in withdrawing the MMR vaccine: autism rates in Japan did not fall  after the withdrawal of MMR vaccine. (In fact, they spiked; see graph below.)

Footnotes

Dr. Gorski has previously offered coverage of this paper at the Science-Based Medicine blog, as have many others. My aim was to offer something shorter that might appeal to parents, with more detail that the press coverage but also less technical. Also as writing practice, I guess. Or at least that’s my excuse… Dr. Gorski’s post includes some background on where this notion might have arisen, and so on, that I haven’t covered here.

1. This survey of parents’ attitudes to the New Zealand Immunisation programme (PDF file) includes those who “believe the National Immunisation Schedule starts too early at six weeks.”

2. It’s a concern touted by groups opposing vaccines.

3. I believe there are (a few) more studies again; most of those listed in the linked articles are focused on the MMR vaccine.

4. While I will still write the odd article on vaccine-related issues, you’ll see fewer of them as this is certainly more her ‘patch’ than mine.

5. It can be exasperating. As one reader at Respectful Insolence put it,

Epidemiologists have looked at the *number* of vaccination and the risk of autism… no, no correlation found. So the atni-vaxxers shifted the goal-posts — “It’s the mercury!”

6. Statisticians will quibble: I’m trying to offer a simplified presentation without confusing things too much. This article is for parents who left high school years ago, not scientists!

Other articles on Code for life:

Sources for medical information for non-medics and non-scientists

The Panic Virus

How vaccines work – a primer

Thoughts on, and for, those trying to choose to vaccinate or not

Fact or fallacy, a survey of immunisations statements in the print media

Immunisation then and now

Vaccination – why learn the hard way?

Autism – looking for parent-of-origin effects

Autism genetics, how do you copy?

Seriously, let me give a shout-out to Holly Bik and Miriam Goldstein’s little paper in PLoS Biology, An Introduction to Social Media for Scientists. Leave a copy on the department coffee table for those less confident about use of social media in science, perhaps?

Bik and Goldstein highlight that many academics are reticent about utilizing social media,

In academia, there is often a particular stigma attached to online activities. Actively maintaining an online profile and participating in social media discussions can be seen as a waste of time and a distraction from research and teaching duties. We believe this perception is misguided and based on incorrect interpretations of what scientists are actually doing online.

I have some sympathies, it must seem that way from the gossip about general use of social media. And not helped by the wayward examples the mainstream media highlights!

Really it’s over to your use of it. Some stick closely to work-related issues. Look and you’ll find there are specialist social media sites, just as there are specialist blogs.

I feel it’s more a matter of starting in a smaller way in circles you are comfortable with and working from there. You will want to balance the benefits against the time involved, as they discuss. (I had to laugh at the description for ‘Write for established blog’ or ‘Start your own blog’: ‘Life-Sucking Yet Strangely Satisfying’! Ah, yes… Seriously though, blogging isn’t that bad. I think.)

You should read their tips and, in particular, the potential benefits they discuss, but below are a few casual thoughts of my own. I realise this is unlikely to reach the people it might best target as readers here are already on-line, but perhaps this might encourage those who at the moment are more readers than participants.

• Try pick one form of media first and learn it rather than take them all on at once. With that in mind, when reading Bik and Goldstein’s article, perhaps use it as a guide to the types of media you’d like to explore first.
• Many will find it more comfortable to keep work and private networking separate. I’d recommend that. In one sense, this isn’t entirely possible: work colleagues will be able to, if they put the effort in, locate your personal site and as you get to know people you will naturally make casual comments. But you can at least use (say) a different twitter account for personal stuff, limit your Facebook account to contacts outside of work, use different blogs for work and your political rants (or whatever else). People will know you have interests and contacts outside work so some ‘slippage’ is expected. The question is more one of signal-to-noise: for work contacts too much unrelated ‘chatter’ filling otherwise work-related material can put them off.
• Do browse around and read new forums for a bit. It helps to get a feel for what’s considered the form before jumping in. As you get more experienced you’ll be able to jump in more quickly.
• Don’t feel (too) shy about asking people things – one of the key elements of social media is it’s much more a level playing field than many flesh-and-blood meetings with their social hierarchies. (Don’t feel offended if popular people don’t write back – most likely they’ve just got dozens of others writing to them.)

I’ll get out of the way and let you read their paper. Readers are welcome to offer their experiences and tips in the comments below.

Other articles on Code for life:

GoPubMed — PubMed browsing using ontologies

Forward to wikipedia – topic pages in computational biology

Choosing an algorithm — benchmarking bioinformatics

Nature’s reproducibility effort: when to get data specialists on board

Literate and test-driven programming (in bioinformatics)

I’d like to draw attention to one point ArsTechnica’s coverage of this development noted that has wider impact, outside of this Nature initiative:*

To let certain readers know exactly how likely a given result is, Nature will now provide the authors with a statistician to consult (which, really, they should have arranged for themselves before even writing the paper). Authors will be encouraged to provide the underlying data for any charts or graphs in the paper.

This is too late in the act for the research, although understandable from what Nature is trying to achieve for itself and the relationship with the wider public.

The time to start getting the statistician, the computational biologist or other ‘data’ specialist involved isn’t before writing the paper or even when you start the work, as one commenter there wrote, but when you write the grant application.

You want them involved from the onset so that they might help design a sound project. Hopefully the grant application will fare better too. You want to them to head off problems in the research before they turn into headaches, not to have your data team ‘make do’ with whatever data was collected.

I’d like to think larger projects in, say, genomics have long got their head around this one (we hope), but equally I suspect a lot of smaller projects still try tackle the data as it occurs, which is essentially after-the-fact.

Returning to the Nature initiative, some are questioning the effort it might involve both scientists and reviewers. Personally, I’d rather have more complete methods. It’s very frustrating when an aspect isn’t made clear. It reminds me of a loose saying that a project (or computer program) isn’t complete until it’s properly documented. It also reminds that generally it’s easier—and better—to document as you go along. Lab notebooks** are the start everyone uses but what’s needed is something that communicates to someone not familiar with the project.

On alternative that one commenter mentioned is,

That said, Nature tends to be almost more in the style of magazine articles these days. Its more about the audience than the content. Ideally, you would submit an overview paper to Nature, and refer to a more detailed paper for people who want to dig deeper into it. That way, you (a) get two papers out of it, and (b) you don’t turn off all the people who read Nature that aren’t even remotely in your subfield.

It’s an interesting point but personally I wonder if it’s better done in a more science + science-communication fashion with paper kept as papers, with all the detail they need, with lighter ‘reader’ pieces for those with a less focused interest in, say, an on-line magazine format (or science blogs).

There’s also Nature encouraging researchers to provide the data behind graphs, etc. In the interests of time, I’ll not explore this here (but feel free to share their thoughts on this below if you wish to).

The discussion at ArsTechnica is worth reading if this topic interests you – it’s got a pretty good signal to noise ratio.

Footnotes

It’s worth remembering Nature has an extensive supplements section, should it be needed. The alterations are to the Methods section.

* I have to admit I wonder what they mean by ‘certain readers’.

** Someone is bound to mention open notebooks, so I will here! I’m also reminded of literate programming.

Other articles on Code for life:

Reproducible research and computational biology

External (bioinformatics) specialists: best on the grant from the onset

Developing bioinformatics methods: by who and how

Retrospective–The mythology of bioinformatics

You still have to know how the tools work

Bioinformatics – QC, reproducible, statistical and sequence-oriented