The World Is Magical

Arthur C. Clarke famously wrote:

Any sufficiently advanced technology is indistinguishable from magic.

An excellent quote to be sure, but wrong. And here’s the reason: There is no meaningful difference between magic and science. Stick with me for a minute.

Magic, to be useful, must operate under some rules. We may not know them (as people in the real world or as readers of fiction) but without rules magic simply wouldn’t be very interesting or useful. Gandalf figured out or was taught how to do things. Harry Potter had to go to school to learn the arts of magic. If the magic envisioned in these fictional accounts didn’t adhere to rules it would be pretty useless, right? You can imagine that there may be influences from outside the magician or spell-caster (for example some source of magic that they have to return to, or something similar). And there could be stochastic influences that might render spells useless once in a while. These also are rules and principles. So magic, to be useful, must follow rules.

If you accept that magic has to follow rules (not necessarily the rules of science as currently understood, mind you) then these rules have a basis- a fundamental, underlying structure that allows them to function. And allows witches, warlocks, magicians, and whoever to access them and make use of them. If there is an underlying fundamental structure then humans, using reasonable and careful approaches, should be able to figure out these principles.

How would they do this? Well they would first make a guess about how the magic should function (a hypothesis)- that saying “exploso lignum” and moving your wand in a circle should make wood explode- then test that hypothesis- cast that spell- then evaluate the results. Did the results support the hypothesis?

So magic, as an operating principle of this or a fictional world, can be figured out by a method that is, in fact, the scientific method. Therefore, once you can apply the scientific method, the object of your study is just science. Of course, if your hypothesis isn’t supported (for example, that subjects can correctly identify symbols on cards that are held by another person and not shown to them) then it isn’t magic, and it isn’t science. It isn’t anything.

Science is just a way of figuring out how the world functions. And if one of the organizing structures of a world is magic, then science would be able to figure it out. So any magic we can imagine must be just science (once the rules governing it have been figured out). Note that invoking a divine power doesn’t get around this- the divine power still has to obey rules, even if they can change those rules (how do they decide to change a rule? we should be able to figure that out).


Gandalf, the scientist.


The $1000 paper

[Updated 11/2/2014 with green open access and NIH PubMed central caveats]

Anyone familiar with the debate around open access scientific journals knows that it can be expensive to publish your work there (see this list of some publication charges). In one model of open access publication the cost is shifted to the authors, who are usually funding publications from their grant money, and those charges can be in the thousands of US dollars per paper. The Public Library of Science (PLoS) journals charge between $1300 and $2900 per article, though they have a program for partial to full coverage of these charges. The result is that anyone can access, download, and read the paper free of charge opening up the research to a much wider audience.

During the Twitter discussion of alternative scientific metrics spawned by the so-called “Kardashian index” paper (see my post here) some metrics regarding publishing were suggested. One that was suggested to me (though unfortunately who suggested it is now lost in my Twitter feed- sorry) was to create a metric that calculated how expensive a paper would be to read, if you didn’t have institutional or other subscriptions to the publishers.

Here are the assumptions used:

  1. No access to any subscriptions
  2. You would purchase every paper/chapter cited in the paper
  3. You would pay non-student prices (where applicable)
  4. You’d buy the book if you couldn’t purchase individual chapters
  5. Updated! Pointed out by  that I forgot one very important caveat. Many of these for-pay papers may be available as “green open access” (self archiving their own publications) or by requirements such as those imposed by the NIH that require deposition of papers in the PubMed Central repository.

This is actually an interesting idea – and it’s only taken me about 5 months to get to it but I calculated numbers for three papers (see Table and full spreadsheet here).

The bottom line is that it would be EXPENSIVE to read a single paper this way, over $1000 for each paper (with the caveat that I’ve only looked at 3 papers total).

 Table showing cost of citations for three papers
Summary Journal Total number OA Average cost Total cost
Paper 1 PLoS Computational Biology 37 5 $38.43 $1,422.05
Paper 2 Nature 27 3 $27.87 $752.50
Paper 3 Journal of Bacteriology 41 3 $38.71 $1,587.22

This has a linear relationship with the number of citations in the paper as demonstrated in this graph (again, small sample size).


Of course, this is mostly an academic exercise (like most things I do- I’m an academic) since nobody reads every citation and most people who want to read specific citations would have access to institutional subscriptions. However, it points out a hidden cost to research publication that (I don’t think) is thought about by most researchers.

It would be fairly simple to code up a calculator for this metric given that many journals are published by the same publishers who have pretty consistent pricing. But I’ve got to get back to work now and publish more papers.



Who should we blame for the Ebola infections in the US?

[Disclaimer: I have a PhD in microbiology which DOES NOT make me an expert in epidemiology or in disaster preparedness or in health care policy in ANY way. However, I have formed OPINIONS which are backed up by some reports (mostly anecdotal at this point) that I refer to in this post. If you have differing opinions or can cite evidence that my assertions/suggestions are incorrect or misleading please do so in the comments section. The standard disclaimers apply as well- this is my opinion and does not reflect the opinions of my employer or the employers of anyone in my household.]

Short answer: Everyone and no one.

Longer discussion: There has been a lot of blame thrown about recently in regard to the recent US Ebola infections. Currently there have been three cases, two where the infections happened here, and the third was diagnosed here. When the first nurse who cared for Thomas Duncan, the Liberian man who was diagnosed with Ebola in a Dallas hospital on Sept 30th 2014 (see CDCs continuously updated timeline here), contracted Ebola the director of the CDC, Tom Frieden, addressed this stating:

We don’t know what occurred… but at some point there was a breach in protocol and that breach in protocol resulted in this infection.

With this statement the blame was set clearly on the nurse (and then subsequently, nurses) who “breached protocol”. Dr. Frieden has since explained that he did not intend to blame the nurse in this case, however, the idea is still very much resonating in the media. President Obama stated yesterday (Oct 15th):

If we do these protocols properly, follow the steps, get the information out, then the likelihood of widespread Ebola outbreak in this country are very, very low. But, I think what we’ve all learned over the last several weeks is that folks here in this country and a lot of nonspecialized hospitals and clinics don’t have that much experience dealing with these issues (my emphasis)

And summarized the problem nicely. There were no protocols. There are lots and lots of hospitals in the US. There are likely VERY few of them that had Ebola-level protocols in place with trained staff prior to the patient in Dallas. This INCLUDES the Dallas hospital itself prior to Mr. Duncan’s case. Why would they? Prior to that occurrence there were no Ebola cases in the US. What would make the administrators at that hospital wake up one morning and think- “you know what, I’m going to put in place an expensive and time consuming set of protocols and train my staff on them for something that is highly unlikely to occur here and that just by undertaking this will make everyone in the hospital and the community panic”. They wouldn’t.

So the “protocols” referred to by the CDC, the president, and the media EXIST in the world  and are very effective (see below) but DO NOT EXIST at most hospitals in the US. The nurses at the hospital in Dallas (anonymously) have stated that there were no protocols in place, that there were inadequate supplies for the kind of protocols that need to be there and that there was generally confusion and disorganization around the entire process. You should read this, because it nicely summarizes the situation (though anonymously and anecdotally). Here are a couple of quotes I’ve selected to give the flavor:

No one knew what the protocols were or were able to verify what kind of personal protective equipment should be worn and there was no training.


There was no advance preparedness on what to do with the patient, there was no protocol, there was no system. The nurses were asked to call the Infectious Disease Department.  The Infectious Disease Department did not have clear policies to provide either.


Initial nurses who interacted with Mr. Duncan nurses wore a non-impermeable gown front and back, three pairs of gloves, with no taping around wrists, surgical masks, with the option of N-95s, and face shields.  Some supervisors said that even the N-95 masks were not necessary.


Hospital officials allowed nurses who had interacted with Mr. Duncan to then continue normal patient care duties, taking care of other patients, even though they had not had the proper personal protective equipment while caring for Mr. Duncan.


Were protocols breached? The nurses say there were no protocols.

Reports that the nurses were wearing protective gear and following protocols but still got infected has caused fear, suspicion, and general confusion. “If the CDC is being truthful with us how could this happen?” “Maybe it IS airborne and they just don’t want us to know!” “That nurse should have been more careful” “Those hospital administrators should be prosecuted” (these are statements extracted from my own interactions with people about this subject, discussions on social media, and general tone of the media coverage- not actual statements people have made).

The truth is that there ARE protocols for taking care of these kinds of patients. They have been developed and tested during this and previous Ebola outbreaks in Africa by groups like Doctors Without Borders. These protocols ARE effective and have been tested many, many times under much more difficult conditions than those faced in normal US hospitals. President Obama addressed this in his recent statement and backed it up by hugging and kissing staff who had treated Ebola patients at Emory University hospital in Atlanta- WHERE THESE PROTOCOLS HAVE BEEN USED because they knew the patients were coming from Africa to be treated there. The protocols WILL protect healthcare workers who have to take care of Ebola patients in US hospitals. They NEED to now be proactively implemented by hospitals around the country as soon as possible- but that doesn’t mean that every staff member in every hospital has to be trained extensively or provided access to protective gear. This only needs to be done for a small number of staff that could be designated responders. The CDC has stated that they will send Ebola ‘SWAT teams’ to hospitals with confirmed cases. An educational program should be in place in all hospitals to make sure that administrators and supervisors know where to turn if they suspect an Ebola case and what to do in the short term. This is good preparedness policy.

Things are changing because of the situation in Dallas and this is good. But they need to change more and more quickly in order to prevent the same thing from happening when the next Ebola patient arrives at Providence General in Portland OR, or Lakes Region General Hospital in Laconia NH, or Kadlec Regional in Richland WA, where I live.

So who to blame because we have to blame someone?

The CDC? Maybe, but they are struggling to manage a very complex and evolving situation that has not really been faced in the US previously. The scale currently is very, very small-  infections in two out of 300,000,000+ people. However, there will be more as the outbreak in West Africa continues- and a nightmare scenario of a larger-scale outbreak in the US may be unlikely, but is not out of the question by a long shot.

The nurses? Nurses in general are not prepared for handling this kind of patient. In some areas of the hospital they are trained for handling MRSA, TB, and other infectious diseases, but the protocols and protective equipment for those are insufficient for handling Ebola. “But why did the second nurse hop on an airplane? Isn’t that completely irresponsible? Why didn’t anyone stop her?” Apparently she contacted the CDC prior to her flight because she had a low-grade fever (below the threshold called for Ebola) and the CDC didn’t advise her against the trip (though they have come out with statements now saying that she should not have taken it). The hospital she worked at may have assigned her to other patients following her taking care of Mr. Duncan- why wouldn’t she then be able to travel? The CDC is also considering implementing a travel ban for all staff who’ve taken care of an Ebola patient.

The hospital administration? Not really. Clearly at this point all major hospitals in the US should be on alert and implementing training for protocols to handle this and making sure that supplies are available. It may be unlikely that most of these hospitals will ever see an Ebola patient (let’s very much hope that is the case)- but something can be done with little cost and effort. Appointing a central contact for Ebola, making sure that an established protocol is present, making sure that there exist protective supplies for at least a small number of staff, providing information to areas of the hospital on what to do if a case is suspected. This is just good preparation. If it’s not used for Ebola maybe it would be used for the next outbreak- and a situation like the one in Dallas could be avoided.

Ebola itself? OK, there. Here’s your scapegoat. Ebola is to blame.




The Mad Scientist Confectioner’s Club

Boxed truffles I made a couple of years ago.

Boxed truffles I made a couple of years ago.

So some of you might be wondering why my blog is named The Mad Scientist Confectioner’s Club since I mostly post about science-y and academic subjects. Well I also make candy. Mostly I make truffles every Christmas for friends and family and I’ve been doing that for nearly 30 years now- hopefully this year I’ll actually get around to posting recipes and procedures I use for those. I also like to make other kinds of candy and bake and cook (here’s a link to the recipes I’ve made up and posted).

I titled my blog (and my Twitter handle too, @BioDataGanache) this way because I see parallels in confectionary willy_wonka_1and science. Blending ideas, using simple ingredients in complex ways, working and reworking recipes, and producing something cool and sweet in the end (hopefully).

or this post I’ve collected a whole list of amazing and science-related candy from around the WonderWebs, channeling up a little bit of the old Willy Wonka. Enjoy!

Holo-frickin-graphic CHOCOLATE!

Holo-frickin-graphic CHOCOLATE!

Holographic chocolate

This is really the recent news item that inspired this post in the first place. This is from a Swiss company that uses specially-developed chocolate molds (like, something that you shape with, not the fungus) to etch microstructures on the surface of the chocolate. These microstructures reflect light in a certain way to give the colorful 3D pattern. Very cool science.

The color-changing flavor, Xamaleon. (Credit: Manual Linares, Cocinatis)

The color-changing flavor, Xamaleon. (Credit: Manual Linares, Cocinatis)

Ice cream that changes colors

OK- so not a candy, but I’ll make an exception for this really cool (cold) confection. A physicist developed this ice cream that changes colors in response to changes in temperatures and pH (acidity) – which means that it changes colors when you lick it! I guess that the trick of how this is done is something he’s not revealing, so hopefully it’s not toxic or anything.


poprocksPop rocks

No, eating these candies while drinking a coke won’t blow your head off (at least I don’t THINK it will)- but these, now vintage candies are still pretty interesting. According to this post they are made by allowing the sugar to crystallize under high-pressure CO2. This causes pockets of the harmless gas to be trapped inside the candy. So when it starts melting in your mouth it makes a popping sound as the gas is released.

Syrah ice cream in mid-mix

Syrah ice cream in mid-mix

Wine-flavored ice cream with no alcohol

A winemaker near Portland Oregon used some enological magic to create a wine ice cream with no alcohol and no sugar. I’m not sure how this is accomplished, and I actually like the alcohol in my wine-flavored ice cream, though it did make the freezing process a bit more difficult. Here’s a link to my attempts at making a Syrah ice cream along with my recipe.


3D printed confections!

So the idea of a 3D printer is that a print head is controlled by a computer and extrudes some kind of substance that is liquid in the machine and then turns solid after it leaves. For the standard 3D printers this is generally some kind of special plastic, but why not food? In fact MIT students have created a 3D printer that actually prints ice cream! I’ve linked to the video here:

I like the diagram of their contraption to do this too- it really looks like something we would have put together in lab, but ours wouldn’t have produced tasty things. At all.


Of course you can do this with chocolate as well- which might be a perfect medium for 3D printing because of the ability of tempered chocolate to be liquid one minute and semi-crystalline solid the next, with a small change in temperature. This has actually been done enough that there are a couple of companies Choc Edge and Moving Brands that offer 3D chocolate printing services.

Chocolate Brains! Braaaainnnnsss!

This DIY recipe tells you how you can take an MRI scan of a brain- it could be your own brain- print a 3D latex mold, and make up some chocolate brains that are anatomically correct (at least from the outside). Cool and creepy.

Chocolate zoetrope

A chocolate company in Australia made this incredible chocolate cake that has an animated scene when it spins. I’m betting that some of the parts of the cake might be good to eat, but others might be mostly for show- any cake that is capable of withstanding the g-forces necessary to spin it at high speed may not be that great to eat.

Magic Shell

The ice cream topping is indeed pretty magical. If you’re not familiar with it it’s a syrup that comes in several flavors. Shortly after you drizzle it over ice cream it hardens up forming a crunchy chocolate (or other flavor) shell on the top. According to Chow, the secret of the magic probably lies in the coconut oil in it. Coconut oil is very high in saturated fats, and these will be liquid at room temperature but a solid at lower temperatures. Probably the magic is in how this transition point is tuned with other ingredients in the bottle- normally coconut oil is a solid at 70° F, which might be warmer than some households.

Chocolate itself

Chocolate itself is pretty amazingly complicated. The chemistry of chocolate is complicated; it contains many different compounds including an alkaloid called theobromine, that is a stimulant and a vasodilator, meaning that it increases your heart rate and dilates your blood vessels. In humans theobromine is actually somewhat toxic- you could, in principle, die from an overdose of chocolate. I think that would be pretty unlikely since the LD50 (the dose of a compound that is lethal in 50% of patients) is about 1000 mg/kg – so if I (at ~95 kg) ate dark chocolate (~400 mg theobromine/oz) I would have to eat about 237 oz (the equivalent of about 155 Hershey’s bars- if they were made of dark chocolate) before I would be in the LD50 range. On Amazon I could buy 99% dark chocolate for $4.50 for 3.2 oz- making it about $350 to buy enough chocolate to possibly kill me. Of course, eating all that chocolate would be really difficult. If I were a dog (and about 30 kg) it would take a lot less since the LD50 is 300 mg/kg- so about 9000 mg or about 20 oz of dark chocolate- still a lot, but if the dog is determined (or much smaller and determined) it could be an issue.

It’s history is complicated as well. There was no chocolate as we know it today until about around 1847. The process of making powdered chocolate by removing half the fat and adding alkaline salts to cut the bitter taste was developed by a Dutch chemist in 1828. This produced what is known as Dutch cocao. Soon after, in 1847, Joseph Fry found that he could make chocolate paste by introducing the cacao butter (the removed fat), back in to the chocolate. This has some interesting effects in terms of what you can do with the chocolate.

Tempering chocolate is the process of melting the chocolate to a temperature that breaks the cacao crystals (yes, crystals) then cool the chocolate back down to allow the proper form of crystal to form. It’s a nitpick process that has caused me hours and hours of frustration. However, if you do it right you can then dip your centers (like the truffle ganache) in the pure, tempered chocolate and it will form a hard coating that has a characteristic glossy look to the outside and has a ‘snap’ on the teeth. If you mess up, even by a couple of degrees when you’re reheating the chocolate for dipping you’ll end up with untempered chocolate in your truffles. These will dip great (even easier than tempered chocolate- maybe too easy actually) and will cool to look fine, but then hours to a day later they’ll form streaky grayish lines on the surface and the consistency will be bad- kind of powdery and grainy. The weird thing about it is that the cacao butter in the chocolate (which is some kind of particulate suspension is my guess) can take on about six different types of crystal form (I’m pretty sure they’re using the term ‘crystal’ loosely here). And each of these has different properties for appearance and texture. Amazing. The photo I use for the header of my page is one I took of tempering chocolate.

Light-up lollipops

And here’s one more for the DIYers. You can make your own light-up lollipops. Sounds like tasty fun!


So thanks for hanging out with me and exploring the intersection of two of my favorite things, candy making and SCIENCE! (OK, so some of it is actually engineering and not really science at all, but still) If you’ve got suggestions for additions let me know in the comments.



A Fine Trip Spoiled

I had a dream the other night that inspired this comic. My dream was about waiting for a connecting flight. I decided to take it easy and do something fun, then realized that my flight was leaving soon and I was nowhere near the gate. Then I got on a train and realized I was going the wrong direction. Anyway, I woke up to the realization that I’d relaxed and done fun stuff most of the weekend (I did work some in the evenings) and that I had an unfinished grant that was still due this week. As it turned out I finished up my grant quite nicely despite the slacking off- or maybe even because of the slacking off. But it gave me the inspiration for this comic.

You see, writing and submitting a grant proposal is a lot like planning for a vacation that you’ll probably never get to take. The work you’re proposing should be fun and interesting (otherwise, why are you trying to get money to do it, right?) but your chances are pretty slim that you’ll ever get to do it- at least in the form that you propose it. I’ve started to think of the grant process as a long game (see this post from one DrugMonkey)- one where the act of writing a single grant is mainly just positioning for the next grant you’ll write down the line. Writing grants give you opportunity to come up with ideas, to consolidate your thoughts, and think through the science that you want to do and how you want to do it. The process can push you to publish your work so that you can cite it as preliminary data. And it can forge long-lasting collaborations that go beyond failed proposals (though funded proposals certainly help to cement these relationships in a much more sure way).

I think “A Fine Trip Spoiled” may be the title of my autobiography when I get rich and famous.


Literature Search Party

Continuing on my adventure metaphor theme: has this ever happened to you? You have a great idea, it’s brilliant, it’s revolutionary, it’s a thing that will change the way that people think about other things. You work on it, sometimes feverishly. And get… great results! Then you think, “hey – wait a minute. If this is such a great idea and so simple, why hasn’t anyone ever thought of it before?” Pause about 10 minutes. “Ohhhhhh… no. They probably have.” A quick PubMed search turns up that seminal paper from 1995 demonstrating what you’ve just ‘discovered’. My diagram on how to do science highlights this point.

Anyway, why does this problem happen and how can you avoid it. I don’t have the answers but here are some general ideas.

For me this often happens because, in coming up with a brilliant new idea you’re pushing your knowledge and experience past it’s limits. In the early stages this means that your ideas are not very well formed; you don’t have a clear idea of what you’re thinking about and how it might relate to other things. And you don’t know the area you’re moving in to. So even doing a literature search at this point can be useless. I’ve had the situation where what I was searching for actually had been done before, but I didn’t know what to call it- so PubMed was useless.

After you’ve started to get some legs to the project, maybe doing a few tests to see if it would even work and getting positive results, excitement can take over. Then you just want to get through it and get the good results. Even then you may not be able to see your idea in a greater context to be able to know what to look for.

Finally, in the later stages of the project you can suffer from “investment blindness”. You may ignore the issue of searching the literature because what if you found that you weren’t doing something new? You’d put SO much work in to it, it would be unthinkable to have to abandon it all! And you’re on a roll- the good results are coming in, the implications are starting to fall into place, and the shape of the thing, the idea you’ve had, is starting to make itself clear. It’s generally at this point that that creeping, nagging, suspicious feeling comes up. Yep, you’re pretty sure somebody MUST have done this before.

Sometimes you’re wrong. Other times you’re right, but the spin you’ve put on things and the results you’ve gotten are actually novel and you can still get a story out (this is the most common actually). Then there are the times when there’s just nothing you can do. Your exact idea has been done somewhere else and published in Nature or Science or Cell, Nature, and Science.

I guess the idea is that you know your field so well that you can see the gaps and know when you are trying something new. That’s true of a number of different projects I’ve initiated. Generally, these are not the most interesting or groundbreaking. Sometimes they’re downright boring, small steps forward.

How can you prevent this? I guess by being aware of that three-step progression I outlined above, and trying at each step to do your literature searches with that in mind. Also, be pessimistic: always start from the point of view that someone has done it before. You’re then not surprised if they have done it, and you can start to evaluate how different and novel your approach is from theirs. Approaching your literature search from the point of view that you’re looking for something will make it more likely that you will find something.

Also, consult friends and colleagues who are working in similar areas. Sometimes they may know what you’re talking about – that is, that someone has already done and they know the name of what it is you’re doing. Sometimes they might just be able to provide you with a sounding board for your idea that will allow you to clarify your thoughts.

Above all, be flexible. If it turns out that someone has done it before read their paper carefully and any follow-on papers you can find. Look for the gaps and ask how what you’ve done can answer a critical question they’ve left open.

Dude. You want a beer or something? It's hot work making it all the way up here.

Dude. You want a beer or something? It’s hot work making it all the way up here.