Monday, February 27, 2017

Death of the stethoscope?

By Font Awesome by Dave Gandy -, CC BY-SA 3.0, LinkIt’s not just zombies that rise from the dead—science news stories can also come back to haunt the reader.

Take “Death of the stethoscope,” which surfaced in my RSS feed in the middle of 2015. As a former stethoscope user, the clickbait headline immediately intrigued me.

No stethoscope? How would clinicians survive?


First off: a little history. According to his Wikipedia summary, a French doctor called René Laennec invented a hollow hearing tube in 1816 to assist doctors in listening to a patient’s heart and lungs. Around 1852, the single tube morphed into the standard model that you see plugged into physicians’ ears from Grey’s Anatomy to House to ER. Apart from making them look hot professional, a stethoscope also helps with auscultation, the examination procedure whereby a doctor eavesdrops on your internal whooshes, pings and lub-dups. Noises from heart rhythms, gut movements and respiration all help with making a diagnosis since a lot of this internal chatter is very specific.


According to the headline(s), the humble “manual” stethoscope is on the edge of obsolescence in the medical world, facing a high-tech upgrade to or even replacement by hand-held devices that apparently do the job better.

The Motherboard post on adopts its title from Adel Birbari’s article of the same name, published in the Lebanese Medical Journal in 1999. It suggests that clinicians favour high-tech USB-powered digital over rubber tubing, echoing a point in a press release from the World Heart Federation released the previous year. An article in the Washington Post from January 2016 repeats the call for replacement with something more appropriate to the digital age.

The number one contender to replace the stethoscope is a portable, hand-held ultrasound device, but this is closely followed by digital adaptations ranging from electronic versions to the Eko CORE, a digital add-on that works with the traditional stethoscope to amplify and record sounds. By Põnn [CC BY 2.5], via Wikimedia Commons Practicalities

While it is refreshing to learn that technology has not passed over such a basic piece of diagnostic kit, I do have some concerns about encouraging clinicians to dump the familiar neckwear or even to abandon the professional skill of auscultation.

As a former practising veterinary surgeon, some of these reservations do have a practical component.

  • Distance: Number one for me is that being at the earpiece end of a stethoscope removes my face somewhat from the immediate danger zone, whether fanged or hoofed. Apparently, this also is why Laennec came up with his idea, though he was more interested in staying away from the heaving bosoms of well-padded female patients than avoiding bites. Medical doctors celebrate the contact stethoscope auscultation brings with the patient; most vets prefer to maintain a safe zone.
  • Expense: Veterinary patients are notorious for not respecting boundaries. Electronic stethoscopes and their digital alternatives cost a lot more than a standard manual model. Would I want to brandish hundreds of dollars’ worth of hearing tube wannabe in a muddy farmyard cattle crush, or dangle it over the open ocean? No; nor would my boss be happy with me for risking the practice profits. As a side note, how many clinicians in marginal communities or developing countries can afford more than the perfectly functional basics?
  • Convenience: The alternatives might be hand-held, but they all need power. Where’s the electrical outlet in a remote cow byre? And how many battery changes are required to complete a herd health visit? Just my luck that the battery would fade just as I homed in on a crucial diagnostic squeak in the consulting room. My ears don’t wear out unless they are enjoying a Pet Shop Boys concert.


But am I just being a luddite?

I checked with some of my peers through Facebook. Most of them are still in practice and therefore see life at the sharp end. Would they lose the stethoscope and swap the traditional for digital, I wondered? By Tim1965 [Public domain], via Wikimedia Commons Of the seven who replied, three mentioned that electronic stethoscopes received as gifts remained unopened, unused and unloved. One reason given is that veterinary use is a very small market, and stethoscopes designed for human use, even with pediatric sizing, are often not refined enough for diagnostic work in cats, for example. Three large-animal vets mentioned problems with cost for both maintaining the equipment and dealing with damage or loss in the field.

Q: Just wondering if any large-animal vets would carry around a $350 stethoscope out in the field.

N:  No. We have 45 vets who regularly lose things! And out in the field there is seldom a power source. We power our scanners with good rechargeable batteries, but they are $500 to $800 each.

J: Just the basic stethoscope. Although they will sometimes use their rectal scanner on the chest wall if they think there is a pericardial effusion. All cows.

C: And have left/lost/damaged plenty of kit on farms. … So prob would avoid if expensive.

Only one vet regularly uses the electronic version, commenting that it lasts for ages on a single AA battery. He also mentioned it was a great boost for mild hearing loss, this last point echoed by an internal-medicine teacher at a vet school.

Three vets commented on using scanners as alternatives, with one describing the hand-held option as useful for cage-side assessments but lacking the detail of larger machines. Another mentioned that cattle vets often reach for the rectal scanner when suspicious of pericardial effusion (fluid build-up around the heart)—hand-held yes, but probably not what was envisaged in the articles!

So maybe not such a dinosaur then.


The topic resurfaced again in the last year, with a news story on the CBC/Radio-Canada website and an interview with Dr. Raj Bhardwaj on the Calgary Eyeopener radio program. Dr. Bhardwaj mentions the same high-tech replacements and benefits but does bring up the subject of cost—around $200 will buy you a stethoscope, but you need $8,000 or so for an ultrasound device—and fragility.

Stethoscopes bounce…

…as does the story, which, like the instrument itself, refuses to die.

The post Death of the stethoscope? appeared first on Talk Science to Me.

from Amanda – Talk Science to Me

Tuesday, February 21, 2017

Fear of brave new worlds or uninspired headline writing?

capek_rurSummer 2016 marked the 85th anniversary of novelist Aldous Huxley completing his manuscript for Brave New World. The widely read novel, a dystopia of happiness-led oppression (in contrast to the fear-controlled populace in Orwell’s 1984), anticipates global adoption of advances in science and technology such as subliminal learning and reproductive medicine. Published in 1932, the book is still a popular read, ranking fifth in Modern Library’s list of the 100 best English-language novels of the 20th century.  Unsurprisingly, its title, along with Orwell’s, has also become a stock phrase in headlines, used to signal a new direction for advances in science and technology.

“Test-Tube Babies: The ‘Brave New World’ of Human Pregnancy Is Coming!”
The Evening Independent, July 22, 1978
Designer babies, grow a baby in a bottle and more.

“Brave New World: Will gene editing rewrite the future of medicine?”
Genome, n.d.
Engineering disease (and other things) out of humans with CRISPR.

“The Brave New World of Three-Parent I.V.F.”
The New York Times Magazine, June 27, 2014
Heritability, and who is the parent?

But there’s a twist—since Huxley presents these advances purely as societal methods for keeping people under strict control, should writers only use the words as a subtle suggestion of imminent doom?

Fear sells

And why not—bad news sells! A pessimistic slant draws in the reader, especially since wariness about subjects such as artificial intelligence (AI) translate into great plot lines, such as Agent Smith’s battle against Neo in The Matrix. Hollywood scriptwriters over the years have run and run with the theme of AI and machine learning allowing computers to overtake their human overlords, creating some truly memorable moments on screen.

…and it’s certainly difficult to shake off such technopessimism when it’s reinforced by Stephen Hawking and Elon Musk!

Technopessimism justified?

Nevertheless, does scientific advancement truly deserve the “brave new world” tag? Is it all doom and gloom? Looking at AI and science in particular, there are benefits, and wariness shouldn’t be automatic; AI already helps scientists with their research.

At IBM, we are guided by the term “augmented intelligence” rather than “artificial intelligence.” It is the critical difference between systems that enhance and scale human expertise rather than those that attempt to replicate all of human intelligence.
IBM’s Response to a White House RFI: Preparing for the Future of Artificial Intelligence

While there are many stories of how advances in AI impact daily life—from robots for senior care to the self-driving Google car—available for public debate, there are also many less publicized advances helping the day-to-day life of your average scientist. These include search platforms that sort through primary research papers, and bioinformatics, where software tools manage data analysis for busy scientists.

Every 20 seconds, a new scholarly article is published in biomedicine, resulting in more than 1.5 million per year.
Introducing Meta Science,

AI for science

Before creating data, scientists must first stay current with what’s happening in their subject. This means keeping a close eye on publications. Since very few studies hit the big time of widespread media coverage, researchers need to use online tools to compile reading lists of relevant primary research papers and journals. In life sciences, the weekly publication rate is overwhelming, and a simple query on PubMed, the United States National Library of Medicine’s searchable index, returns dozens of hits. Sorting through these for relevance is extremely difficult and time-consuming—it used to take me several hours every week to stay up to date.

However, new search tools such as Meta Science help researchers navigate through this complex soup by constantly ranking and comparing papers. Instead of just pulling up any article that matches the search term, Meta Science retrieves only those that are highly relevant, using AI to constantly scan and score publications as researchers both publish and cite them in other papers. Another platform, Bioz, does something similar: it ranks experimental procedures, reagents and instruments cited in papers, freeing up research time for actual experimental design

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.

Another major time crunch for researchers is data crunching; there’s a lot more of it these days to analyze. Modern laboratory instruments throw out many more results, and automation means that multiplexing sample analysis is common. The spreadsheets of old simply don’t cut it anymore in these data-hungry days.

Many of the papers I reviewed for the Accelerating Proteomics blog involve software tool design, helping researchers zip through the vast arrays of data coming from modern mass spectrometry. When spectral data files regularly run to gigabyte ranges, researchers need powerful software that cuts through the noise to make sense of peptide identification and quantification. In bioinformatics, researchers, statisticians and mathematics wizards collaborate to create algorithms that make data analysis easier and faster at the click of a mouse.

In the world of protein chemistry, tools such as PREGO make quick work of multiplex assay design. This program designs serial reaction monitoring (SRM) assays, using existing data sets to select the “best performing analytes” for the job. It thus bypasses the rounds of tedious manual selection, testing and validation normally required in assay development, improving SRM performance in addition to freeing up research time. Another program, Novor, allows real-time readouts from peptide fragments zipping through a mass spectrometer, bringing proteomics up to the same speed as genomic sequencing. No more waiting for results.


Talk Science to Me client and biomathematician Shelly DeForte uses bioinformatics to study protein structure and protein disorder and its influence on functionality. She creates algorithms that pair structural assessments of amino acid sequence with functional behaviour in enzymes and other proteins. In silico modelling replaces the need to run multiple assays to measure activity and function.

In her most recent paper, algorithms were used to classify missing regions in protein structure databases. Instead of manually poring over each instance of irregularity in the Protein Data Bank, DeForte and co-author Vladimir Uversky’s bioinformatics tools automatically pick them out for further study and analyze the patterns of disorder seen over multiple absent sites. Work that would take days to eyeball now occurs in a click.

Machine learning is a method of data analysis that automates analytical model building. Using algorithms that iteratively learn from data, machine learning allows computers to find hidden insights without being explicitly programmed where to look.
Machine Learning: What it is and why it matters

These few examples show that scientists definitely benefit from advances in technology: without bioinformatics tools such as PREGO, they would be back to crunching the numbers manually to interpret data. Added to the hours spent hunting down relevant papers to read, this manual analysis cuts down on productive hours in the lab and delays results. Furthermore, since many of these tools also use “scary-sounding” machine learning to teach themselves and improve functionality, the speed and accuracy just keep getting better and better.

The verdict

So, wariness justified or not? Technopessimistic or techno-optimistic? I’d suggest optimism, since gaining efficiencies in lab operation and data analysis is a positive benefit. Definitely not doom or gloom.

Time to rethink “brave new world” as a stock science headline?

Huxley originally meant his title as an ironic statement about the society the novel portrays. As Maeve Maddox suggests in Daily Writing Tips, maybe we writers should use it “only in a context of dehumanization or oppressive surveillance.”

Okay, I suppose automation is a form of dehumanization, removing the hands-on element from search or analysis. Also, #confession: at times I did feel “controlled” by my lab schedule; however, at no point did I feel that the thermal cycler was watching me.

Let’s stop using “brave new world” to signal new frontiers in science, or anywhere else for that matter…unless we’re truly being oppressed!

The post Fear of brave new worlds or uninspired headline writing? appeared first on Talk Science to Me.

from Amanda – Talk Science to Me

Wednesday, February 15, 2017

Around town: Operation Med School

Medical students learning from professor.This one’s for you if you have a high school student around the house who is thinking that med school could be a good option for post-secondary.

A group of enterprising Grade 11 and 12 students is putting on a one-day pre-medical conference for high school peers. Run as an annual event, Operation Med School exposes attendees to many aspects of working in health care by giving them a chance to meet medics, biomedical researchers and other professionals in the field of medicine. The Vancouver event takes place on Saturday, February 18, at the Robert H. Lee Alumni Centre of the University of British Columbia. (The team also runs similar events in Toronto and Calgary.) Admission includes a lunch card as well as networking opportunities with people who can help guide a future medical career.

Dear reader, I’m sure if you cast your mind waaay back (or even waaaay-er back for some), to those intense days of career planning for high school graduation, you will no doubt remember the heady mix of giddy excitement at the prospect of adulthood mixed with a good dose of nervous anxiety at making the wrong choice.

If you were lucky, you or your parents knew someone working in the field of your dreams who could give you the lowdown about it. They, or maybe a careers advisor, might have also suggested some pre-admission work experience to try the job in action and make sure of your choice. University admissions departments gave out information on how to apply; career mentors showed you how to make your application stand out through volunteering, school course choices and extracurricular activities.

And if you were really lucky, your contacts could always come up with some really juicy on-the-job horror stories in an effort to put you off.

Although gory, this is also important.

In medicine, knowing that you are not going to faint at the sight of blood is a big plus. For veterinary medicine…well, it’s more appropriate to know you could deal with poop and foul smells, both in close quarters. Just saying…

Sorting out post-secondary choices can be confusing, depending on resources available. Events like Operation Med School are a useful one-stop career shop, giving practical insight from professionals into what a career in health care might look like and topping it up with advice on how to get there.

By offering a glimpse into the medical world, Operation Med School promises students a day filled with lectures and hands-on activities…probably not the red stuff, though.

Operation Med School
Saturday, February 18, 9 am to 5:30 pm
Robert H. Lee Alumni Centre, 6163 University Boulevard, Vancouver, BC  V6T 1Z1

The post Around town: Operation Med School appeared first on Talk Science to Me.

from Amanda – Talk Science to Me

Friday, February 10, 2017

daily snapshot: February 10, 2017 at 07:20PM

Finding my happy place
from instagram

In case you were wondering: HeroRATs

Tuesday, February 07, 2017

Electronic Health Records: A New Ethical Issue for Biobanking?

via Inside Biobanking

Electronic Health Records: A New Ethical Issue for Biobanking?

via Inside Biobanking
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