A Skeptic Over Coffee: Young Blood Part Duh

Does this cloudy liquid hold the secret to vitality in your first 100 years and beyond? I can’t say for sure that it doesn’t. What I can say is that I would happily sell it to you for $8,000.

Next time someone tries to charge you a premium to intravenously imbibe someone else’s blood plasma, you have my permission to tell them no thanks. Unless there’s a chance that it is fake, then it might be worth doing.

Californian company Ambrosia LLC has been making the rounds in publications like the New Scientist hype-machine to promote claims that their plasma transfusions show efficacy at treating symptomatic biomarkers of aging. Set up primarily to exploit rich people by exploiting younger, poorer people on the off chance that the Precious Bodily Fluids of the latter will invigorate the former, the small biotech firm performed a tiny study of over-35s receiving blood plasma transfusions from younger people. It’s listed on clinicaltrials.gov and everything.

First of all, to determine the efficacy of a treatment it’s important that both the doctors and the patients are blinded to whether they are administering/being administered the active therapeutic. That goes all the way up the line from the responsible physician to the phlebotomist to the statistician analyzing the data. But to blind patients and researchers the study must include a control group receiving a placebo treatment, which in this case there was not. So it’s got that going for it.

To be fair, this isn’t actually bad science. For that to be true, it would have to be actual science. Not only does a study like this require a control to account for any placebo effect*, but the changes reported for the various biomarkers may be well within common fluctuations.

Finally, remember that if you assess 20 biomarkers with the common confidence cutoff of p=0.05, chances are one of the twenty will show a statistical difference from baseline. That is the definition of a p-value at that level: a 1 in 20 chance of a difference being down to random chance. Quartz reports the Ambrosia study looked at about 100 different biomarkers and mentions positive changes in 3 of them. I don’t know if they performed statistical tests at a cutoff level of 0.05, but if so you should expect on average 5 of 100 biomarkers in a screen to show a statistical difference. This isn’t the first case of questionable statistics selling fountain of youth concepts.

All of this is not to say that the experiments disprove the positive effects of shooting up teenage PBFs. It also generated zero conclusive evidence against the presence of a large population of English teapots in erratic orbits around Saturn.

You could conclude by saying “more scientific investigation is warranted” but that would imply the work so far was science.

* The placebo effect can even apply to as seemingly objective a treatment as surgery. Take this 2013 study that found no statistical difference in the outcomes of patients with knee problems treated with either arthroscopic surgery or a surgeon pretending to perform the surgery.

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A skeptic over coffee: sick of lab meetings

rhinovirus

This post brought to you by a dedicated community of human Rhinovirus ( pdb model 1AYM).

Imagine the following dialogue between researchers:

Wayne the Brain: “Third one this week ::Cough:: I am literally sick of lab meetings.”
Wankdorf: “Oh I feel ya. There are way too many lab meetings. It’s a real waste of time, but that’s the cost of pulling from so many different realms of expertise in interdisciplinary projects.”
Wayne the Brain: “No no no, I am literally sick of lab meetings. All the exposure is really taking a toll on my health. ”
Wankdorf: “Why didn’t you say so?! Stay away, you purveyor of vile pestilence! ::cough::”

I hope, dear reader, that you spotted the root cause of their misunderstanding. Wayne (the Brain) was hypothesizing a suspected transmission rate while simultaneously advertising his own condition as definitely infected and possibly contagious. Wankdorf (unsurprisingly) misinterprets the statement by applying a more colloquial definition of the term “literally.” It’s not clear whether infection of the second researcher could have been avoided and the spread of the disease slowed had they practised more effective communication, but that scenario is plausible given what we know.

Of course this is an extreme example, and the consequences may not always be so dire. The most frustrating part of the above exchange and subsequent misunderstanding is that neither participant was strictly wrong in the definition they assumed for “literally.” This word now literally can be used to say “in the truest sense of the words” and the exact opposite, and my brain literally imploded when I learned about the new definition.

If you don’t believe me, check out the definition in both the Cambridge and Merriam-Webster online dictionaries. I’ve screenshotted the definitions to preserve this embarrassment for posterity:

merriamwebsterliterally

cambridgeliterally

Language is dynamic, some (Wankdorf etc.,) would even say that it is dynamical. Hence it doesn’t make you appear smarter to bore your friends by talking about Romans every time they say “decimate.” Language is constantly changing in response to the selective pressures of popular usage, subject to many factors as people and cultures interact.

Similar to many other examples of evolution, humans affect the way a language changes by taking note of and modifying the selective pressures they individually exert. The consequences may be particularly important in science, where English is the common tongue but not in general the first language of most practitioners. I expect that modern English will evolve to encompass multiple forms based on usage. Native speakers sat on the British Isles, laying in North America, and so on will continue to retain and invent complexity and idiosyncrasy, while international English will come to resemble a utilitarian version of Up-Goer Five English, paring off superfluous complexities while retaining the most effective elements to become as simple as possible, but no simpler. It’s possible that international English will even retain sarcasm.

Pop quiz: what’s your favourite English speaker idiosyncrasies used in this article?

A skeptic over coffee: who owns you your data?

AskDNA

“Everyone Belongs to Everyone Else”

-mnemomic marketing from Aldous Huxley’s Brave New World

A collaboration between mail-order genomics company 23andMe and pharmaceutical giant Pfizer reported 15 novel genes linked to depression in a genome-wide association study published in Nature. The substantial 23andMe user base and relative prevalence of the mental illness provided the numbers necessary to find correlations between a collection of single nucleotide polymorphisms (SNPs) and the condition.

This is a gentle reminder that even when the service isn’t free, you very well may be the product. It’s not just Google and Facebook whose business plans hinge on user data. From 23andMe’s massive database of user genetic information to Tesla’s fleet learning Autopilot (and many more subtle examples that don’t make headlines), you’re bound to be the input to a machine learning algorithm somewhere.

On the one hand, it’s nice to feel secure in a little privacy now and again. On the other, blissful technological utopia? If only the tradeoffs were so clear. Note that some (including bearded mo. bio. maestro George Church) say that privacy is a thing of the past, and that openness is the key (the 23andMe study participants consented that their data be used for research). We’ve known for a while that it’s possible to infer the sources of anonymous genome data from publicly available metadata.

The data of the every person are fueling the biggest changes of our time in transportation, technology, healthcare and commerce, and there’s a buck (or a trillion) to be made there. It remains to be seen if the benefits will mainly be consolidated by those who already control large pieces of the pie or to fall largely to the multitudes making up the crust (with plenty of opportunities for crumb-snatchers). On the bright side, if your data make up a large enough portion of machine learning inputs for the programs that eventually coalesce into an omnipotent AI, maybe there’ll be a bit of you in the next generation superorganism.

aSOC: Plant physiology (on Mars?)

Mars_23_aug_2003_hubble

Hubble Space Telescope image of Mars

Several months ago Andy Weir’s The Martian showed up on the feed of personalised advertisements for Kindle books on my account. No surprise, I read tons of sci-fi. Preferably no magic or dragons, as I can only tolerate so much “any sufficiently advanced technology is indistinguishable from magic.” So-called “hard” sci-fi tends to be the what I like most, and I gravitate to authors that have a propensity for characters on “the spectrum” or that are artificial intelligences (::ahem::). In any case, I read the sample from Amazon for the ebook, and I didn’t get into it.

Then last Wednesday Randall Munroe mentioned it was a cool story on xkcd. So I read it, and it was awesome. It’s a story about a guy fixing things in space. The flippant personality of the protoganist (Mark Watney, aka Matt Damon) is actually a tried-and-true literary device used to explain technical concepts to readers without being patronising. There’s a specific name for it that my exocortex is failing to bring me right now, but in any case, Andy Weir goes a long way to make sure his story is technically legit.

But this is aSOC, and I have to mention at least one thing I think was a mistake. And that thing is: space potatoes. Watney’s official job description entailed two roles on the mission to Mars: botanist and mechanical engineer. These are bascially the two skill sets most likely to enable someone to survive after being abandoned on another planet, which is a convenient coincidence for our buddy Mr. Damon. He grows potatoes and (oh sorry, spoiler alert starting a few sentences ago) at one point he worries about “suffocating” the potatoes by leaving the space house for a few days, thus not providing the plants with the CO2 they need to “breathe.” One problem: plants don’t breath CO2.

Don’t get me wrong, plants definitely need CO2 to make triose phosphates, sugars, starches and cellulose, etc., but this isn’t what they “breathe” on a cellular level. Plants need to respire just like we do to power aerobic metabolism. Plants need CO2 for photosynthesis, not respiration. A metabolically active plant doesn’t photosynthesize at night, but in general it will still need a low level of oxygen to survive. And I sure would have liked to see an energy balance for his indoor Mars farm. Photosynthetically active radiation on old Terra is about 300 Watts per square meter, and I’d be surprised if the reading lights in his space house are up to the task of meeting that level of output.

In any case, I can recommend that you go ahead and read the book, maybe watch the movie later, and think about space some more.

A Skeptic Over Coffee #1: Starter Kit

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It takes effort and maintained vigilance to become an effective skeptic, with the penetrating mental focus to cut through the misleading. Honing one’s questioning acuity means hardening one’s mental defenses against charlatans, fraudsters, and the merely incompetent in all walks of life. With practice it’s possible to be the infamous “Reviewer Number 3” who gradually gets fewer and fewer invitations to provide peer-review for “paradigm shifting” articles from editors of high-impact journals. It may seem like a grandiose dream, but you too can in fact be the colleague who corrects the university press office’s outlandish claims about their own paper, causing their tenure review to be shelfed for another year (for failure to be interviewed on Science Friday</a<). If this glamourous lifestyle of modest claims and bold negations sounds appealing, read on!

I invite you to join me every once in a while to practice skepticism in these short segments designed to provide about one coffee's worth of skeptical inquiry. My day job pushing things around with lasers both takes a lot of time and requires that I drink a tremendous amount of coffee, so the concise aSOC format should fit right in with my new lab-monkey lifestyle.

Here is your Beginning Skeptics’ reading list:

  • A seminal paper by John Ioannidis runs the numbers on an over-abundance of false-positives in the scientific literature.
    John P.A. Ionnidis. Why Most Published Research Findings Are False. PLOS. (2005). DOI: 10.1371/journal.pmed.0020124

  • Retraction Watch is an important resource for any skeptic. If someone consistently publishes retractable articles and no one notices, does anyone lose their scientist licence?
  • Jeffrey Beall runs black lists of predatory publishers and journals taking advantage of pay-for-publish open access models atScholarly Open Access. Also consider John Bohannon’s misleading report generalising predatory practices by OA publishers and ensuing criticism of his approach.
  • And remember your statistics:
    http://xkcd.com/882/
    Why it Always Pays to Think Twice About Your Statistics
    An investigation of the false discovery rate and the misinterpretation of p-values

  • UPDATE: Recent, interesting consideration of widespread inflation of scientific results.
    Megan L. Head, Luke Holman, Rob Lanfear, Andrew T. Kahn, Michael D. Jennions.
    The Extent and Consequences of P-Hacking in Science.
    PLOS. (2015) DOI: 10.1371/journal.pbio.1002106