Friday, December 20, 2013

Podcast: Isotope Ecology

New podcast episode!

On this episode we are joined by Patrick from the podcast "Science, sort of" to talk about isotope ecology. There are some great things we talked about including how much fossils can really teach us. Before recording this episode I assumed that fossils only really gave us structural information (in other words, what a dinosaur looked like). As it turns out we can learn a ton about extinct animals from isotopes. Come listen!

3:00 - What is isotope ecology and what types of questions can isotopes help us answer?

8:00 - Distributions of heavy water. Preferential evaporation and raining of different isotopes of water.

12:30 - Crocodilian evolution as studied by isotope ecology. When did saltwater tolerance come into play?

20:30 - Patrick describes the process of analyzing the isotopes he collects.

25:00 - Was T-Rex "warm" or "cold" blooded?

35:00 - When was the first time whales started living in the ocean?

43:00 - Fortnightly scientist

Monday, December 9, 2013

Podcast: Interviewing my 4 and 6 year old sons

New Podcast!

Check out this quick podcast where I ask your science questions to my 4 and 6 year old son. Thanks for your questions!

Tuesday, November 26, 2013

Podcast: Carmen Drahl

New podcast episode!

Sam and I interview Carmen Drahl. She talks about a recent article about Chris McCandless ("Into the Wild"). How did he die and what does chemistry have to do with the story?

Show Notes

1:30 - Carmen tells the story of Chris McCandless from the book "Into the Wild" (Her article HERE).

9:00 - Chad fumbles the pronunciation of beta-ODAP

11:00 - More mispronunciations - Lathyrism is basically limb paralysis, a pretty deadly condition for someone alone in the wild like McCandless was at the time.

14:00 - The chemistry story deepens - where is beta-ODAP found? (My apologies for the phone ringing)

19:00 - So how did Chris die? Apparently (unknown source) Chris was cremated so any of these tests can't really be done.

20:00 - Carmen doesn't trust her mother. What a cynical woman (I say this in jest, of course. I've been burned in the past by bad sources, so I understand the importance of what she's saying).

20:15 - A great quote. I'm not surprised that Chemjobber was the one to find the source.

22:30 - Ben Goldacre, author of  "Bad Science" and "Bad Pharma" is mentioned. Ben is an amazing author, scientist, and speaker. Check out his books.

24:00 - Group Think.

28:00 - Inserted audio from Futurama - "You have a degree in bologna"

28:15 - Scientific rigor in the pharmaceutical industry.

29:00 - "Everything is a chemical". We're hitting all the cliche things that chemists talk about in one episode. 
We also talk about the gray area in the "Natural vs

36:00 - Chemists telling bad jokes. Followed by a bad segue.

38:00 - The Fortnightly Scientist - Carmen talks about Detective Monday from Mathnet.

42:00 - Carmen is far too optimistic about the reach this little podcast has. She describes an "outpouring" from the science community after we air this podcast. I do appreciate the comment, Carmen, but I don't think we're there yet.

43:00 The Fibonacci parrot

46:00 - Carmen is seriously disappointed that I haven't watched "The Wire" yet.

Tuesday, November 19, 2013

Learning to Be Offended

I am a man born in the United States to two white, religious, upper-middle class parents.

In other words, I've been dealt a pretty good hand. Much like Louis C.K., I don't mean that to brag - I'm just being honest. Never in my life have I missed out on an opportunity because of my race, gender, beliefs, or financial situation. This doesn't mean that I've been able to do everything I've ever wanted, but I pretty much started life with every door open to me and began closing them when I decided I didn't want to walk through them.

But I've learned to develop empathy. I self examine. I don't want to be racist or sexist but I'm not very well equipped to answer the question "Is this racist?" or "Is this sexist?" because I've never experienced either personally. As a white male my perception of racism and sexism must be defined by the minorities that experience them.

And that's not an easy thing to do. 

I remember telling a very racist joke in high school. I thought it was hilarious and thought my friends would enjoy it. It didn't even cross my mind that one of the listeners was of the race I was joking about. Some of my friends laughed, but only when I met her gaze did the situation become apparent to me. I still feel the sting of embarrassment just thinking about it.

And so my perception of racism and sexism has had to change through the eyes of others. My natural perception is that nothing is racist and nothing is sexist because I'm culturally favored in both. But, through either my mistakes or the mistakes of others my perception has changed. In other words, I've had to learn when to be offendedThat may sound strange to some. Many say that being offended is something to "get over", so why would I make a conscious effort to be more offended? 

Remember that my natural state is to be offended at nothing. Learning to be offended has helped me comprehend when things I say are hurtful to others. I benefit from this by not looking like a jerk but more importantly I hurt people less often.

I've done a lot of learning in the past 3 months. Not because of anything I've said or done, by watching others. The incidents involving Danielle Lee and Bora Zivkovic began a tidal wave of stories from women in science sharing their stories. On Twitter, #ripplesofdoubt united men and women sharing how they have been affected by sexism. Others shared their stories on blogs. I was touched by every story. I was becoming offended with them and it wasn't really about anger. I felt hurt with them. It's a powerful experience to feel hurt for things said about someone you don't know. 

This past week I saw video by Joe Hanson from "It's Okay To Be Smart". It's a horribly sexist video featuring bobble-head Marie Curie. I'd like to point out in great detail why I find it offensive. 

Joe, and PBS, here are some things I think you need to learn to be offended about:
  1. 0:44 - Marie Curie's introduction begins the sexism. Although she is the only one at the table to have won two Nobel prizes she says it was "very nice to be included". Like she owes something to the men at the table. This comment, on it's own, wouldn't be too bad but the entire video follows this same tone.
  2. 0:53 - When Isaac Newton introduces himself we hear Marie Curie's voice ask "Who are you?" - I'm sure Marie Curie new who Isaac Newton was - she won a Nobel prize in Physics! Now, I suppose it may have been sarcasm on Marie's part, but I don't understand why. If anyone Einstein, whose theory of relativity greatly expanded physics past Newtonian physics, should have made the comment. As in "I'm Einstein, who are you?"
  3. 1:12 - Einstein begins flirting with Marie Curie. It begins as a harmless compliment, I suppose, but this video is supposed to be about the contributions that each has made to science. This makes it the wrong place to make that joke. In a different video you may have gotten away with it. 
  4. 1:21 - "That's a good one" - No it's not, Joe. It's what starts your video down a pretty dark path.
  5. 1:23 - Marie tries to get Einstein to leave her alone (Joe, do I have to tell you that "no means no"?). Einstein asks Marie: "Wear me like a parka". That's creepy. Again, I suppose in a video whose premise was something like "Einstein is a creepy old man" this might work. But the premise is supposed to be about their contributions. Creepy Einstein takes away from the message. If you need proof just look at the reaction to the video. People aren't talking about contributions they're talking about the awful jokes.
  6. 2:25 - Joe and Marie talk about the difficulties that women face in science. Okay, so good news is that Joe understands the problem. But wait, isn't this the part where each scientist describes the lasting impact their work has had? So Charles Darwin is a scientist whose contributions matter but Marie Curie is a woman
  7. 3:36 - All these great men did such great things! Again, this probably wouldn't have been a problem if it were isolated. In fact 3:36-4:09 contains a great message that I believe is what you wanted the tone of the video to be. Unfortunately, the actual tone of the video makes it more obvious sexism. 
  8. 4:29 - Einstein exposes himself to Curie. Hey, do you guys remember that time when PBS said it was ok to expose yourself when flirting didn't work?
  9. 4:48 - Einstein rapes Curie. Hey, do you guys remember that time when PBS said it was ok to rape a woman when exposing yourself didn't work?
  10. 0:05 - Bottom left corner, small print non-pology. Telling someone you know they've been offended is a poor way to apologize. It shifts the blame from you to them. It makes it "their problem" instead of "your problem". Own the issue, learn to be offended, and do the right thing.
Now Joe (and I seriously hope you're reading this) I know you've felt attacked this past week. I know you probably feel embarrassed.

That's part of the process. Take that embarrassment and learn to be offended. You've presented the world with a bad video and a lot of people have criticized you. Fix the Problem, Thank Them, Move Forward.

You've also received a lot of support. Many people have rallied around you telling you how funny the video was and how everyone else just didn't "get it". 

Ignore them.

Remember my story from high school? It was the worst, most disgusting joke I could imagine and still some of my friends laughed. There will always be someone willing to laugh at a racist or sexist joke. Be better. Learn to be offended. Write a real apology and publicly ask PBS to take down or dramatically change the video. Learning to be offended isn't about becoming an angry person. It's about becoming empathetic, and I'm trying my best to learn. I invite you to join me.

Edit: Joe has made the decision to take down his video. I applaud the decision. Some say that it was just an over-sensitive vocal minority that caused him to take the video down and that he "caved". I don't think that's the case. I think he realized that the tone of the video wasn't congruent with what his message was meant to be. Kudos, Joe. 

Tuesday, October 29, 2013

Humor in Science: The Ig Nobel Prizes

New podcast episode!

Sam and I interview Marc Abrahams from the Ig Nobel prizes. Marc had some great stories to tell and it turned out to be a really great episode.

Everything discussed can be found at

~1:00 - Chad starts the podcast off by pronouncing the guest's name wrong. Don't worry, that only continues for the entire episode.

~3:00 - How the Ig Nobel prizes began.

~5:00 - How Marc became editor of a magazine that he'd never read before.

~7:00 - Deciding the categories of the prize. Inventing a category name for a prize. I think Sam gives a very good name for the suit of armor to protect against grizzly bears.

~12:00 - Can you try to win an Ig Nobel prize? Marc says no, but plenty of people nominate themselves each year.

~14:00 - How has the description of the Ig Nobel prizes changed over the years?

~18:00 - Analyzing dragging sheep across the floor.

~23:00 - Winner(s) of both the Ig Nobel prize and the Nobel prize.

~25:00 -  What do stinky feet and cheese have in common (chemically speaking)?

~28:00 - Miss Sweety Poo, the cutest solution to a problem every award ceremony has.

~44:00 - Are some of the prizes tongue in cheek?

~50:00 - Chad realizes he's been saying Marc's name incorrectly.

Friday, October 18, 2013

Bora Zivkovic resigned today from his position at Scientific American. 

But you probably already know that. I don't intend to give all the facts about what happened here. I also don't plan on defending Bora; what he did was wrong.

Bora is arguably the most influential person in science writing today. Following him on Twitter over the past year has been informative enough for me that I all but stopped using an RSS feed; If it was good I knew I was going to see it on Twitter anyways. Bora has also been a great personal help to me. I sent him an e-mail about a year ago telling him about my blog and the aspirations I had of being a well known science writer. He took the time to read a few of the things I'd written, gave me some simple feedback, and gave me tips on how to share the things I was writing. Bora leaving Scientific American is a huge blow to the scientific community.

But Bora had to go. Sadly, he had to go for all the same reasons that made him great. He was influential. He guided young scientists and writers. He organized important meetings, tweet-ups, and forums. Someone with that amount of influence and power can't act the way he did and keep that influence.

There might be some that would argue that Bora should stay with Scientific American. They might say the good outweighs the bad. They would be wrong. If he were to stay at Scientific American it would send the clear message that inappropriate behavior is acceptable - as long as you balance it out with a position of power. But remember, it's the position of power that is the problem in the first place.

Influential people aren't immune to criticism, they're the most deserving of it.

Tuesday, October 15, 2013

Computational Chemistry with Professor Chris Cramer

New podcast episode!

In this episode Sam and I are joined by Professor Chris Cramer from the University of Minnesota. Show notes after the embedded player.

Remember, you can also find us on iTunes or just subscribe using the RSS.

All times are approximate (± 2 minutes):

1:45 - What is computational chemistry? Also, my phone goes off right next to the microphone during a question I can't reasonably edit around.

4:00 - Chemistry (or at least computational chemistry) seems to have its own definition of "theory".

5:30 - What types of questions does Chris work on? Chris talks about different scales of calculations: Length, time, and energy. Each of which bring their own insight and problems to the table (computer?).

8:30 - What system have you worked on in the past that you're glad to be done with?

9:15 - Odd projects that are "finished" often launch new research.

9:45 - Collaboration with experimentalists.

13:30 - Computational chemistry as a guide to experiment.

15:00 - Nobel prize in Chemistry.

19:00 - Paul from ChemBark gives his prediction for the Nobel Prize in Chemistry. See the full Google Hangout here.

21:00 - The H-Index

22:00 - Where does computational chemistry go from here?

23:00 - What are the limitations in computational chemistry? Chris talks about messy systems. Do we need more computing power or do we need a new theory?

28:00 - Accuracy in computational chemistry. Chad gives a bad analogy. No really, it's bad (it works perfectly in his head, though).

29:00 - More thoughts about collaboration with experimentalists. The take home: If you go to Prof Cramer and he says "We should write a proposal" it may just be because you haven't thought about it enough yourself.

31:00 - Chris explains what a wavefunction is (with a much better analogy than the one Chad gave).

33:00 - What is the life of a computational chemist like? What should a student do to prepare?

39:00 - Chris brings up the impostor syndrome. Two episodes in a row now. Chad loves nothing more than listing the things he's not good at.

41:00 - Computational chemistry in Sci-Fi boks and movies.

45:00 - The Fortnightly Scientist. Chris talks about grandfather to his children Paul Dowd and his work with Non-Kekulé biradicals. Chemists will love this section. Non-chemists may need the wikipedia article to understand (but it will be worth your time. These molecules are pretty cool).

Thursday, October 3, 2013

Alternative Forms of DNA with Dr. Zoë Waller

We're back with another podcast!

This week Sam and I sat down with Dr. Zoë Waller to talk about her research into alternative forms of DNA, what inspired her to be a scientist (I seriously enjoyed her answer to that question), and the "CSI effect".

Give it a listen, it's great stuff! As always, if you have someone you want to hear from on the podcast please let us know. You can do that here in the comments, by e-mailing chad (at), or find me on Twitter (@thecollapsedpsi).

Timestamps for this episode (all approximate)

1:30 - Zoë gives the basic idea behind her research: Alternative structures of DNA.

12:20 - What is your day to day like?

15:30 - What did Watson and Crick think about their research? (Here's a link to a version of the paper with some interesting commentary. Original paper found here).

19:00 - What are the big unanswered questions in your field?

21:00 - The Fortnightly Scientist: What scientist has been the greatest inspiration to Zoë?

24:30 - People around you in science are important; inspiration can come from many types of sources.

26:00 - How Chad became a chemist. The impostor syndrome. The best science comes from being able to doubt yourself correctly. Here's the article Sam is talking about.

Wednesday, September 18, 2013

What Can Chemistry Learn From Cooking

"Chemistry is just like cooking, just don't lick the spoon"

It's a familiar chemistry joke, but the more I think about it the more it just doesn't seem true anymore. Cooking, as a discipline, is evolving rapidly in the public eye. Chemistry, in some regards, is retreating into the safety of the lab.

Now I'm not saying that chemistry should have the glory that cooking now enjoys. I've said before that while chemistry bloggers love to believe that chemistry gets sunbbed I'm not sure it's true. A chemistry "cook-off" would look more like an episode of Breaking Bad than an episode of Iron Chef. Cooking, and more generally food, is an important part of everyone's life. It's no surprise, then, that people love food shows

. . . or is it a surprise? The early days of cooking shows were programs like Julia Child's. I love her show, but let's face the reality: it wasn't prime time television. Her show was a low budget PBS program. She didn't have millions of viewers and corporate sponsors. So what happened? Why has food become so interesting that it has jumped to the major networks?

I think I found the answer in a recent episode of The Alton Browncast. Alton Brown, the host of said browncast, interviews Ted Allen. They talk about his career, why you should read (not sniff) wine corks, and how food programming has evolved. 

Allen mentions that he tries, in his position on Chopped, to not speak above the audience. For example, if a judge or contestant says something like: 

"That dish just needs some acidity" 

He'll clarify that they mean it could use a squeeze of lemon or splash of vinegar. I understood his comment to mean that he doesn't make the audience a student but instead makes them part of the experience. This isn't the same as feigned ignorance, a common tactic in science. If you pretend you don't know something you can ask the right question of the expert. It works sometimes, but I don't think it's always effective. I think Allen's attitude is what has made modern cooking shows so great. 

That's not to say that Julia Child ignored the audience, or even that she spoke down to them. She had a great personality and was extremely informative. But compare her to, for example, Chopped. Chopped isn't a show about great chefs teaching you how to cook. It's about watching those chef's struggle. It's at its most entertaining when a chef is lost. It's at this point that you're experiencing the process with the chef. There is no finished product waiting in the oven to show off. You don't even know if the chef is going to be able to finish the dish. At this point you have left the audience and entered the competition yourself. 

And that's how you turn cooking from something you see on PBS to something everybody wants to watch.

So what can chemistry learn from this? I think the answer is to make ourselves more accessible. Learn what terminology needs to be explained and learn when to stop explaining. Don't just make chemistry education about showing as many things to as many people as possible. Instead, take people on a journey of science discovery that makes a few pit stops in chemistry.

I think this was the purpose of the "Everyday Chemistry" competition from the American Chemical Society. Take a chemistry concept that is seen everyday and teach people about it; make chemistry apply to their life. Unfortunately I think the competition failed in its objectives. I can say this in a non-malicious way because I was one of the finalists in the competition. I think it failed because while the audience was supposed to be non-chemistry experts much of the contest was directed at chemists. I understand that you can't control what "goes viral". You can speak to your audience but that won't make them listen. This is especially true on the internet. The ACS seems to focus a lot of their outreach programs on talking to chemists.

There's a very thin line that separates dumbing down from speaking above, but it's a line we need to walk if we really want to see chemistry in the mainstream. It's this line that I hope to walk as The Collapsed Wavefunction moves forward. The podcast is doing well and I hope to keep improving the content. I feel like that's the place I can contribute the most to science outreach. Sam and I have several experts scheduled to speak with us that we are very excited to interview. From their interviews we hope to present something that is accessible to a wide audience while still being entertaining. We're hoping to bring real research results, not generalized statements, to podcast form. It's going to be a blast, so stay tuned.  

Tuesday, September 17, 2013

BAH Fest: Humor in Science with Zach Weinersmith

New podcast episode!

Zach Weinersmith, the mind behind SMBC-Comics, sits down with Sam and I to talk about The Festival of Bad Ad-Hoc Hypotheses. This was a very fun episode to record and I hope you enjoy it. (NSFW-ish).

Remember, you can subscribe to our podcast on iTunes or any other podcasting service (RSS here). We'd love your comments, iTunes ratings, or any other feedback. Send e-mails to:
chad AT 

Show Notes:

~1:45 - Zach tells us about the BAH Fest - Link to the website which has the comic that we're talking about.

~8:45 - Organizing BAH Fest. Zach was worried that only 50 people would show up to his 500 seat venue.

~9:30 - Bombings postponed the first planned BAH Fest.

~15:00  - What is the connection between humor and science?

~18:00 - Zach talks about how he got into making webcomics and how he became a physics major as a way to create stress in his life that would lead to better comics.

~23:00 - The aquatic ape hypothesis.

~26:30 - Zach talks about naked mole rats.

~26:45 - Zombie ants and other mind controlling parasites.

~31:00 - Another example of what to expect at the BAH Fest.

~34:00 - Zach tells us about SMBC comics and how its content has changed to match what he's doing in life. Here's the comic that I refer to (which is, in my opinion, his best comic to date - if you include the red button image).

~39:45 - Fin. Zach complains about anti-red-head-ism.

Monday, September 9, 2013

BWONG! - Viruses with Kevin Bonham

Another podcast! Kevin Bonham joins us once more to talk about viruses.

Thanks for listening, and as a final plea: If you like the podcast (or at least tolerate it) head over to iTunes and give us a review and five stars. If you don't like the podcast, or have suggestions for improvement or future episode ideas, send an e-mail to chad (at)

If you'd like to subscribe to the podcast, but just can't stand iTunes, you can do that using this link:

or you can always just listen right here:

Show Notes

2:40 - Kevin explains the (not so) easy question of "What is a virus?"

8:46 - What virus would you not wish on your worst enemy? Kevin talks about rabies and hemorrhagic viruses like ebola.

18:06 - Sputnik, a virus that infects viruses. Bad inception joke. BWONG!

21:40 - Sam begins a long string of questions, all leading to a bad pun.

22:20 - Chad makes a bad analogy to chemistry. Kevin, not a chemist, corrects him on the chemistry. Embarrassment ensues.  

25:01 - Is a virus alive? What's the point of defining it as living or non-living?

29:36 - Transposable elements. Boxes that shut themselves (video here).

30:19 - Prions, the zombie makers.

31:25 - The fortnightly scientist: Charles Janeway.

Tuesday, September 3, 2013

Be part of The Collapsed Wavefunction Podcast

Hello internets!

Sam and I have been working to make our podcast, The Collapsed Wavefunction, even better. Please take a minute to hear what we're planning and help us out.

Please, share this podcast with your friends, give us iTunes reviews, and keep listening; we've got some great stuff planned.

Thursday, August 22, 2013

Sam is an agave hipster: Food science

New podcast episode!

Last week Sam and I sat down with our good friend Aaron Andersen, who recently graduated with a BS in Food Science, to talk to him about food, preservatives, eggs, and synthetic meat. Enjoy!


Show Notes:

Topic; Food Science
Panel: Chad Jones, Sam Matthews, and Aaron Andersen

Sunday, August 18, 2013

Chemistry from an outsiders perspective

Fellow chemistry bloggers/enthusiasts: Let's take a look at this whole "chemistry doesn't get any love" thing the best way we can. I would like to officially submit the following paper for peer review (that is, for review by my chemblog peers). Please understand before you read the sarcastic nature of my writing in this format...

A study of Google search results to understand the public's perspective of chemistry 
Chad Jones
The Collapsed Wavefunction


This article is presented (at least in part) as a tongue-in-cheek look at the public's perspective of chemistry. Chemistry bloggers often remark that chemistry is poorly featured in mainstream science communication. To assess the validity of this claim a Google search results experiment was performed. This experiment showed that chemistry fairs just about as well as physics and biology. To further test the claim, content on the social media webpage "I F***ing Love Science" was analyzed and categorized by discipline. This study shows a high bias towards biology and astronomy on IFLS.


Whether or not the chemistry is a well appreciated science among the general public is a topic of recent debate among the online chemistry community. Oh et al. have pointed out [1] that no chemists are mentioned in WIRED Magazine's "101 Signals", which lists the " reporters, writers, and thinkers on the Internet". This oversight has restarted a common theme among chemistry bloggers: How is chemistry perceived by the general public?[2][3][4][5]

The experiment herein described was performed as an attempt to quantitatively answer that question. Specifically, it has been designed to test the accessibility and visibility of chemistry as compared to other disciplines.  For the purposes of this study "accessible" is defined as "perceived as being easily understood" and "visible" is defined as "featured often in popular culture". Thus a discipline that is both accessible and visible is one that is seen often by the public and is thought of as being easy to understand. The results of this study should be used to shape the future actions of chemistry advocates. If chemistry as a discipline is indeed seen as inaccessible to the general public then specific efforts are needed to make topics in chemistry more accessible. On the other hand, if the science is accessible but not visible then efforts should be focusing on spreading chemistry as it is already presented.


To assess the public's opinion of chemistry as a whole a Google search experiment was designed. This experiment is designed to take a comparative look on how chemistry is perceived. First, negative search phrases were used for a variety of science disciplines (physics, chemistry, biology, math, and astronomy). The number of search results for each discipline were recorded and normalized to represent a percentage of total search results. Next, positive search phrases were used for the same disciplines. The data were normalized in a similar fashion. Error bars on each result represent a single standard deviation from the average percentage of total search results. While simply counting the number of search results does not perfectly correlate to how people feel about a given subject, it is a good first approximation.

Negative search phrases used:
" stupid"
"I hate…"
"…is wrong"
"…is hard"
"I failed…"
"I can't stand…"
"I don't like…"
"…is dumb"
"I'm too stupid for…"
"I don't understand…"
"…isn't useful"
"…is dangerous"

Positive search phrases used:
"…is awesome"
"…is great"
"…is fun"
"…is useful"
"…is my favorite
"I love…"
"I like…"
"…is the best"

Because the author is a masochist, a second experiment was performed to compare to Google search results. The last 117 posts of the popular science blog "I F***ing Love Science" (IFLS) were categorized as being about Physics, Chemistry, Biology, Math, Astronomy, or other. For counting purposes, jokes about chemistry were considered chemistry content, jokes about physics were considered physics content, etc.

Results and discussion

Figure 1 shows the distribution of negative search results. If chemistry were seen as an inaccessible subject one would expect chemistry to have a higher percentage of negative search results. Instead we see that chemistry, physics, and biology all have about the same number of negative search results while astronomy has a very low negative search result. Math has a very high negative search results. This places math as a very inaccessible discipline.
Figure1 - Distribution of negative search results

Figure 2 shows the distribution of positive search results. If chemistry were not a visible discipline one would expect low positive results. These results, however, show that chemistry is as popular as physics and astronomy. Biology is slightly less popular while math is slightly more popular. It is interesting to notice that math scored high in both positive and negative search results.
Figure 2 - Distribution of positive search results

Figure 3 plots the percentage of content on IFLS with respect to discipline. It is automatically apparent that IFLS shows a high bias to biology and astronomy while featuring very little physics, math, and chemistry by comparison.

Figure 3 - IFLS content

While IFLS is by no means a perfect snapshot of the public's interest, it is a reasonable representation of how an educated general audience feels about science. It should be stated that IFLS has a very large audience. Pictures and comments on the site are spread widely throughout Facebook and other social media. It would be in the interest of chemistry advocates to appeal to Elise Andrew, author of the blog, for more chemistry content.


The author of this study readily admits its limitations. It should not be seen as a final say in this discussion. Instead its purpose is to bring a quantitative look at a real problem. Our goal, as science communicators, should be to make our discipline both accessible and visible.

Acknowledgments: The author would like to acknowledge the irony of contributing such a formal article to the discussion about the accessibility of online chemistry education . . .

As this article is being submitted for peer review, I welcome criticisms that go along with that process. If you have new search phrases you think should be included or any other modifications please comment and I will update the results.

Thursday, August 15, 2013

Significant figures

I recently wrote another article for my blog at about significant figures.

For some reason this simple topic - one that is covered over and over in general chemistry classes - is one that really interests me. I love thinking of new analogies for why sig figs are important, and oddly enough I really liked writing this article.

Chemistry friends please leave a comment or a response on Twitter. I want to know:

What is a general chemistry topic that you never get sick of hearing or talking about?

Mine is obviously significant figures....

Wednesday, August 14, 2013

Well Intentioned Bad Science is Still Bad Science

I recently saw an interesting anti-smoking ad:

Let's see what Picard thinks of this ad:

That's what I thought. You see, molecules aren't miniature monsters with eyes and teeth. I understand why they used that imagery; they want to show how frightening these chemicals can be. I can't really call this chemophobia, because it would not be irrational to avoid putting these chemicals in your body.

This public service announcement is doing a significant public disservice, though. People are highly influenced by what they see on TV. This ad is misinforming viewers on the true nature of chemistry. Worst of all, it doesn't need to be done. Why not show the actual molecules? I'd even be ok with a little anthropomorphism; make the actual molecule look menacing. But well intentioned bad science is still bad science.

Tuesday, August 13, 2013

A Chemist's Thoughts on the MythBuster's Breaking Bad Special

I love Breaking Bad. I've watched each episode as it airs since episode #1. I started watching because of the chemistry. So I was excited to see
HF is an extremely nasty acid, don't let the MythBuster's episode fool you into thinking you won't regret a splash of HF (believe me, I've experienced one). One of the real dangers of HF can be described using the principles that Adam taught.

A very happy moment for anyone interested in chemical education

That explanation by Adam was probably the best chemistry related scenes I've seen on television in a long time. It's great to see chemistry on national television in a positive light. Adam's explanation was both accurate and entertaining and I loved it.

That being said, I think they missed out by not explaining the reason that HF is so dangerous. This may sound counter-intuitive, but it's precisely because it is a weak acid that HF can kill you without warning. As Adam said, HF doesn't release a lot of hydrogen atoms. This means that you can be "burned" by HF without even realizing it. There is a small amount of fluorine released which can bind to calcium in your blood and bones. This releases even more fluorine (Le Chatelier's principle) which binds to more calcium in your bones and blood. Even small HF splashes can lead to death by robbing your body of necessary calcium. HF can lead to a host of health problems, so please don't assume that part of the myth is busted.

I wish the MythBusters would have been more thorough with their HF testing. They were quite thorough testing their "special sauce", but we only got to see 100 mL added to a small sample of meat, steel, linoleum, wood, ceramic, and drywall. Here's the thing: HF is known to etch glass. That's the entire premise for the Breaking Bad episode. The MythBusters test fiberglass later in the episode, why not earlier with the HF? I would have loved to see a full scale HF test, and I think the MythBusters missed the mark by not doing it. It may have taken some extra time to work, but I'm certain a pig, lots of HF, and a fiberglass tub would have gotten closer to a Breaking Bad scene recreation. Sure the pig wouldn't be completely dissolved, but neither was the body.

Instead of a full scale HF test the MythBusters decided to change the acid they were using. Now, the MythBusters wisely chose not to divulge what they used to actually dissolve a body. That's not really the sort of education they're interested in giving, I assume. They did give a few hints about the acid they were using and it should have been clear to most chemists that the nasty "special sauce" they used would indeed eat through a pig like a tub full of piranhas - which it did. I thought the full scale test of their "special sauce" was great. They failed to make one connection, though. The myth of easily dissolving a body in acid is busted because that process is extremely exothermic. Just look at the steam rising from this acid bath.

The mercury fulminate scene was the other myth they tested, and it didn't fare well at all. The myth was easily busted, which is a result I would have expected given the extreme nature of the myth. To defend my favorite show, though, the science was exaggerated as a plot device. As I said in our most recent podcast with See Arr Oh, I think exaggerated science is fine as long as it's necessary for the plot and not too unbelievable.

In the end I give this episode of MythBusters an A-. The only thing I think it as missing was a better treatment of what HF can actually do. They did an excellent job of explaining acid chemistry, which was nice.

Podcast: Bad Science in the Movies

Hello! Last week Sam and I recorded a podcast with the great Dr. Oh from Just Like Cooking. I'm calling the episode "Me-sa Love Lightsabers: Science in the Media". Enjoy!

Show notes:
Topic: Science in the Media
Chad Jones
Sam Matthews
See Arr Oh

Articles mentioned:
The "Finding Nemo" Article

Time stamps on the way...

Monday, August 5, 2013

Organometallic Isomers, Awesome Colors, and Agostic Interactions

There are basically only two reasons I decided to study chemistry: Color changes and explosions. Explosions held my interest for a short amount of time, but color changes have always been fascinating to me. I love watching clock reactions like the Old Nassau reaction. So of course I was fascinated by this recently published work.
Two Crystals: Both alike in conformation in fair PNNL, where we lay our scene
Image CreditPNNL

Published recently in the chemistry journal Angewandte Chemie International (a journal that until 6 months ago I couldn't even pretend to know how to pronounce) is the paper "Isolation of Two Agostic Isomers of an Organometallic Cation: Different Structures and Colors", in which Bullock et al. report a system with some very interesting chemistry.

Before reading this article I hadn't heard of agostic interactions (or I had heard and promptly forgotten), but they really are my kind of chemistry. I love weak interactions. An agostic interaction is one in which a caron-hydrogen bond interacts with a transition metal. These interactions are very weak (<15 kcal/mol), and that's really what makes this paper so surprising to me.

The isolation of two different isomers whose crystals are different colors isn't anything new. We've known for a long time that transition metals create some interesting color varieties. What's interesting in this paper is how such a small change can create such a large difference. The two conformations are very similar - the only difference being a C-C rotation and a different hydrogen forming the agostic interaction.

The difference is highlighted in red. It's not much, really.
Image Credit: Cited paper

Computationally (DFT) the energy differnece between these two conformations is only 0.6 kcal/mol, an extremely small amount. It's enough, however, to produce a very different color. The small change in conformation produces a much larger change in the HOMO/LUMO transition. To me the interesting chemistry here isn't that a violet solution precipitates out both blue and orange crystals (but again, color changes are neat). The interesting chemistry is that very, very subtle changes in this system's conformation lead to such distinct color differences. Colors that are actually at the opposite ends of the visible spectrum.

The work in this paper seems very well done. DFT calculations (including HOMO/LUMO analysis), X-ray crystallography, and IR spectra all agree with the conclusion that this simple bond rotation creates such a stark difference in the properties of these crystals. van der Eide EF, Yang P, & Bullock RM (2013). Isolation of Two Agostic Isomers of an Organometallic Cation: Different Structures and Colors. Angewandte Chemie (International ed. in English) PMID: 23897712

Periodic Table Trends

I just finished writing an article for about trends in the periodic table, a topic I'm obviously comfortable with (and many of the readers of this blog are as well). To be honest I checked the trends with wikipedia and other sources many, many times - worried that somehow I had forgotten them.

It was a chance to rethink about the periodic table, though, which was fun. Mendeleev's work is pretty impressive. Being able to predict new elements the way he did was amazing (and will most likely be the subject of a future article).

So tell me, readers, What do you think is most impressive about the periodic table? What is outdated or needs changed? Do you prefer any of the "alternate" forms of the periodic table?

Friday, August 2, 2013

My first post for Do's and Don'ts of Learning Chemistry

As you may have already seen, I'm the new Category Expert Writer for My first article is now published:

I've taught several hundred freshmen in my short time as a graduate student. Without fail they make the same mistakes - even if I tell them otherwise. This list is basically the advice I give to my new students.

So tell me, internet chemistry friends, What advice do you give? Is there any advice that you give but know it will always be ignored?

Heading in a new direction: The future of The Collapsed Wavefunction

For the past two years The Collapsed Wavefunction has been a major part of my identity. I've devoted hours of my time to writing about chemistry, physics, math, biology, critical thinking, bad science in the movies, and pretty much anything else that interested me.

A few weeks ago I was contacted by a recruiter from They offered me a position as a Category Expert, which I have now officially accepted. You can now find me at

What does this mean for The Collapsed Wavefunction
I have loved writing and managing my own blog. It gave me the freedom to say whatever I wanted to whenever I wanted to. Accepting a "real" writing job means that I now have deadlines, content restrictions, style expectations, and the list goes on and on. This means that I won't have as much time to write The Collapsed Wavefunction (come on, guys, I'm trying to get a PhD on top of all of this!) but you haven't seen the last of me. The Collapsed Wavefunction will still be publishing new articles and the podcast has only just begun.

Don't leave me! I'm still here!

With each post I write for I plan on publishing a follow-up here on The Collapsed Wavefunction. It may only be a link to the article but let's face it - I've always been a pretty sarcastic writer. Keep following The Collapsed Wavefunction for bonus content!

Thank you to everyone that reads my silly little science blog. Being involved with such an awesome community has made this hobby very fulfilling.

Monday, July 29, 2013

Curious George is Richard Feynman: Our Favorite Scientists Part I

Newest podcast episode is up!

Topic: Our Favorite Scientists
Panel: Just Sam and I
Music by Jonathan Coulton

Relevant links: - The SMBC comic mentioned

Friday, July 26, 2013

Bad Science in the . . . Magic School Bus?

Ok, I like to write about bad science that I see in the movies. I think it's fun to use movies to segue into a real discussion about science. Today I was watching The Magic School Bus with my kids and, as usual, I started over-thinking everything. I realize, of course, that The Magic School Bus isn't supposed to be scientifically accurate. It's a way to introduce kids to science (or rather, scientific facts) in a way that keeps them entertained. That being said, I couldn't get this thought out of my head: When the students shrink what happens to their internal organs?

Ms. Frizzle: An administrative nightmare

More specifically I was wondering how blood transportation would work. Here's how normal respiration works:

When you breath in O2 it enters your lungs and makes its way into the alveoli - small pockets in your lungs that fill up with gas (ideally oxygen). There's a lot of interesting gas dynamics that happen here, but I'll keep it short by saying that Ois transported from the gas phase (lungs) into liquid phase (blood).

Ois transported through the body bound to hemoglobin - a metal containing protein that can bind up to 4 oxygen molecules.

File:1GZX Haemoglobin.png
The alternating red and blue colors are to help you visualize the different binding areas. They're really all the same.
Image credit: Wiki commons

So, if Ms. Frizzle's class shrinks down to investigate a flower, bake a cake, or investigate the insides of one of their classmates, the hemoglobin must shrink with them. The binding between oxygen and hemoglobin depends on their size similarities, so when they breath in oxygen it would be unable to bind to the hemoglobin in their body; Asphyxiation would be the immediate result of shrinking. This is the same story with Honey I shrunk the kids. Being small make it impossible to breath.

The only explanation I can think of is maybe there's some kind of school bus magic that shrinks the oxygen down as they inhale. This would actually help explain another problem - how does Arnold suffer from pollen allergies when he's smaller than pollen? If the pollen around him shrinks as he inhales then being small is no cure for his allergy woes. This explanation brings new problems with it, though. If the oxygen shrinks to enter your lungs then it takes up less space (obviously). This means that the pressure gradient between outside your body and inside your lungs changes, allowing more oxygen to flood in - and shrink again. It seems to me that oxygen would flood in your lungs until they burst. 

Hmmm . . . I really didn't think this would end this morbidly.

Of course if we're talking about a Magic school bus I guess "magic" is always a valid answer, right?

Monday, July 15, 2013

Punching down? I don't remember swinging at all.

Over the last few weeks there have been several good blog posts written about chemophobia. I suppose this latest round of #Chemophobia began with the now infamous article (at least in the chemistry world) posted on BuzzFeed - "8 foods we eat in the US that are banned in other countries". Sam Matthews wrote an article for this blog, pointing out some of the same bad science and, of course, Derek Lowe gave a much more detailed debunking soon after. Ash Jogalekar suggested a chemical lobbying organization - he's calling it the National Center for Chemical Education. Chris Clarke, over at Pharyngula, apparently thinks we're all douchebags for making the lame "dihydrogen monoxide" joke. Granted, I don't think he's talking about me. When I have made the joke (which I'll admit is pretty lame) I've made it to a group of chemists, so that can't be considered "punching down" can it? Soon after that post came two great articles defending chemists - one found at Behind NMR Lines and another at Doing Good Science.

The question I'm left with is this: What is the right way to fight chemophobia?

I certainly don't feel like I've been punching down. I don't spend my time on the internet to mock someone who doesn't have the same education that I do. I'm not trying to get in the "smart kid's club" by proving that I know a lot about chemistry. In fact I've been very upfront - I don't think I'm incredibly special or inherently smart. For this very reason I think science - to truly be science - must be clear and easily communicated. That doesn't always mean it will be easy to master, but science is designed to simplify, not complicate, our universe. It is the universe - not science - that is hard to understand.

Onto chemophobia, then. How do we tell someone they are wrong without making them feel wrong. Someone that feels wrong is less likely to accept what you have to say - you haven't countered their argument you've insulted them. Accepting that you're right means accepting your insult. I think it's important, and I've said it before, that we don't belittle someone that is most likely just misinformed.

That's why I don't think the "but everything is a chemical" argument is very persuasive - someone using the word chemical instead of toxin isn't using the word chemical in a "everything is a chemical" kind of way. If you're convinced that chemical always means "all matter in the universe" take a look at this picture:

Thanks to Sam for this photo

Unless you can look at this picture and honestly say that Wal-Mart has correctly labeled their brooms and mops you must admit that "chemical" can have more than one meaning. Colloquially it means something closer to "toxin" or "harsh cleaner" or "industrial additive". You get the idea. It usually does mean something that you don't want to ingest.

Often when I see #chemophobia on Twitter it really just comes down to a vocabulary misunderstanding. If the only problem with an article is the misuse of the word chemical, then maybe we should let it go. Perhaps we, as chemists, are a little too protective of our namesake. If the public understands chemical to mean "toxin" then we need to acknowledge that - not mock it. Go ahead and point out that everything is a chemical (by your definition at least), but don't let that be the end of your argument. Continue on to point out why the specific chemical in question is not bad for you (or whatever the case may be).

It's a bit of tightrope that we walk, though, and sometimes we over-correct. Let's face it, chemicals can be very bad for you. Sometimes, in the midst of our #chemophobia rage we seem to be forgetting that - or at least trying to ignore it. Most of the things that the public labels as "chemicals" probably are toxins. My guess is that Wal-Mart, in the picture above, meant to stock bleach, ammonia, and other cleaners under that sign. I wouldn't suggest drinking any of those. We say nothing when ammonia is called a chemical (because, well, it is a chemical). The word chemical, then, becomes associated with bleach, ammonia, and industrial strength solvents. That association makes it difficult to teach someone that aspartame is a chemical but you can drink a diet soda just fine. Chemical is already so well connected with toxin that it's not always an easy task.  

I think we (chemists) really are in a bit of a tight spot. Ash may be onto something - we really might need to start up the National Center for Chemical Education. I don't think it's a simple solution, but it may be the right solution.

But whatever we decide to do just stop throwing punches, ok?