Science Friday - Feathered Dino, Clinical Trials, Coffee Extraction. Jan 24, 2020, Part 2

Episode Date: January 24, 2020

Before any new drug comes to market, it goes through a time-consuming process. Researchers have to recruit human subjects for a clinical trial, collect all the data, and analyze the results. All of that can take years to complete, but the end result could be worth it: a drug that treats a rare disease or improves patients lives with fewer side effects.  Or the opposite could happen: The drug doesn’t have any effect or makes patients worse. So the question is, how is the public informed of the outcome? One answer is ClinicalTrials.gov, a public-facing website where researchers are required by law to register all currently ongoing clinical trials and report their results. That way, the public is kept informed. However, two recent investigations of ClinicalTrials.gov reporting practices show that many researchers aren’t posting their results online. In fact, up to 25% of studies never seem to have their results reported anywhere. And government agencies aren’t enforcing the rule in ways they’ve promised—with heavy fines and threats to withhold funding from institutions that don’t comply. In a delicate piece of shale from coastal China, paleontologists have identified a new species of feathered dinosaur: Wulong bohaiensis, Chinese for “Dancing Dragon.” The house cat-sized dino has fierce talons, feathered wings, and a long, whip-like tail with feathered plumes at the end. Ashley Poust, who published a description of the dinosaur in The Anatomical Record, says it’s “hard to imagine” the wings being used for flying. But he says the wings could have been used to arrest leaps or falls, or to hold down prey while killing it, as modern-day birds sometimes do. In this conversation with Ira, Poust talks more about the dino’s possible lifestyle, and how it fits in with other feathered reptiles. A cup of coffee first thing in the morning is a ritual—from grinding the beans to boiling the water and brewing your cup. But following those steps won’t always get you a consistent pour. Researchers developed a mathematical model to determine how the size of grind affects water flow and the amount of coffee that gets into the final liquid. Their results were published in the journal Matter. Computational chemist Christopher Hendon, who was an author on that study, talks about how understanding atomic vibration, particle size distribution, and water chemistry can help you brew the perfect cup of coffee. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

This is Science Friday. I'm Irafledo. A bit later in the hour. What an investigation of the website Clinical Trials.gov uncovered about drug trial reporting. But first, I'd like to introduce you to the Dancing Dragon. It has vicious talons, feathered wings, and a whip-like twin-feathered tail. And no, it is not a creature from Game of Thrones, but a newly found dinosaur, a bird-like beast packed with feathers and claws and just about the size of a house cat. Here to tell us more is Ashley Pouss, a researcher at the San Diego Natural History Museum in California. Welcome to Science Friday, Dr. Paus. Thank you. It's really a pleasure to be here.

Does it have an official name? It does, actually. So Wulong Bohianza. So the genus name really is Wulong, which is the Chinese words for dancing and dragon. And we really got to that because of the pose of this animal. This is a very small, active little dinosaur. So we wanted something that kind of reflected that. Did you find it in a fossil in a certain pose? Yeah, so this is the type of dinosaur fossil that's preserved relatively intact,

which is a really sort of amazing thing and a really real pleasure to get to work on. But the consequence of that is that they are twisted into these positions that they assumed when they died or perhaps while they were decomposing. And so this one has its head thrown back over its shoulders in a classic dinosaur death pose and its arms kind of folded out in front of it almost like a Russian dancer. It reminded us of the dragon and lion dances from the Chinese sneer, which actually has just started. Now, I said this thing is about the size of a house cat with a long tail, but unlike a house cat, this had long talons. It could do a lot of damage, you think. Yeah, so actually the housecat comparison is pretty great.

So housecats have these retractable claws, right? You know that from having your couch get ruined. But these dinosaurs have really long talons on their feet. And actually, unlike birds, they also have pretty big claws on their hands. So this is definitely a predatory dinosaur, which is reflected in its pointed little teeth. And its close relatives have even been found with different kinds of animals in their stomachs. Oh, wow. Now, it also had feathered wings.

Do you think it could fly that? So that's been a topic of a lot of debate in the community of the... late. We think that they're definitely able to use these wings to generate some amount of lift. So they're able to use the wings in a way, but whether they're doing that to be more nimble, to allow them to be able to maneuver over ground substrate or up into trees, whether they're actually flying or whether they're gliding or flapping while they're falling. There's just an ongoing discussion about that. And hopefully, Wulong is a kind of specimen that maybe can slot into that debate and help others out. But there are other things you can.

can use your wings for, right? Absolutely. And so this is where this idea that you mentioned in the beginning about perhaps it's using it for part of its hunting. Living raptors, often, especially hawks and some falcons, will mantle their prey to hide it from other predators so that they won't try to, you know, steal it, which is a really common thing among living birds. And they also can use the pressure of their wings to sort of create more downward force and pin their prey more effectively to the ground, which would then, of course, dovetail very nicely with use of their claws. This is an idea that was first proposed back in 2009 by a friend of mine, Denver Fowler,

and a group of researchers at Montana State University, where I was a student at the time, and they were looking at why would you still have feathers if you get big, like the close relatives of Wulong, Dynonicus, and Velociraptor, which people might be more familiar with. When you get big, you're definitely not flying. why keep the feathers? And so they thought maybe this might be a way of understanding the origin of these feathered wings. Well, let's talk about that a bit more. So how do you go from having the feathered wings like that and not flying and maybe using it to hold down your prey to, you know, to a flying animal?

Yeah, that's a really intensely interesting thing to a lot of us. I think this transition from dinosaurs to birds has been such a focus of a lot of people's research, not only because these incredible fossils coming out of China really allow us to drill into that. That's data we just never had before, but also because these big evolutionary transitions are such an incredible place to query to get at how evolution actually works

and how you might see the origin of incredible things, such as the flight in birds. So how you get from a wing-like arm to a real wing that's being used for active flapping flight has been a big discussion. And so we think the early steps are that you have to evolve feathers because the bird-like wing is dependent on having

these integumentary structures that grow out of the skin that enlarge and form the major surface of the wing. And then from that, you have to have both the skeletal muscular ability to move the wing in the right way and then as well the wing of a right size to create enough lift. So several things people have determined as we kind of investigate this is that dinosaurs have this huge

shrinking that went on as they, they reached the common ancestor of a dinosaur like Wulong and a living bird. And they also had a pretty interesting set of changes in their brain as they approached the origin of flight. So people are really coming at this question from a lot of different really interesting angles these days. Speaking of interesting, I understand there's a very interesting story behind how you came to study this fossil. You were led astray by another fossil? One of the issues, I think, around the world these days, but particularly in China where there's incredible dinosaurs are being found, is that there's somewhat of a trade in fossils.

People want to buy these things. And of course, my position as a scientist is that the important fossils deserve to be studied and brought out to the public like we're trying to do with our new dinosaur. But a lot of times people will actually alter fossils in order to make them more appealing on the market. And so the first fossil that I got given, I had a great introduction at the Medallian Natural History Museum, which is a big museum in northeastern China. they were really, really welcoming, and they said,

here's the coolest fossil. We'd love for you to study this. I'd been introduced there by my advisor at Montana State, Dave Rikia, who's also a co-author in this paper. And so we sat down with this fossil and we were looking at it. And I was so intrigued because this was a slab that had not only a dinosaur on it,

but another dinosaur and a bird. And so we were thinking, oh, this is going to be the biggest news. The more we looked at it, the more we realized this is a bunch of different pieces of things that had been stuck together. It didn't belong at all. So that was sort of heartbreaking.

We just identified, that's fake, that's fake, that's glued together. And so that really made me gun-shy to work on a lot of these fossils. So we took a lot of care in working with Wulong once we were introduced to it. They were, you know, they said, oh, darn. And then they took us back to look at their incredible collection of actual unaltered fossils that they were very thankful, turned out to be real. So we worked on Wulong. You found it by accident in the back of the collection somewhere. Yeah, so there's this concept, I think, that scientists don't know what we have in our collections, and that's true and untrue.

So I think that there's definitely room for discovery, not just out in the field where hopefully many of us will get the chance to go look for more fossils, but also in museum collections. But that doesn't mean that people have no idea. So the scientists in Dahlian are pretty smart, and they definitely knew these three or four fossils might be something interesting, but even they didn't know that it was going to be a new species. So that was a really interesting moment when we finally looked at it, convinced ourselves that it wasn't fake in anyway, and then realized it was a new tax. Now I understand you have another fossil in your sites right now. Ah, there's a couple different things that we have going on. So I always like to tell people that this is actually the golden age for finding and describing dinosaurs. And I think there's a lot of things behind that.

New technologies, the increase in digital databases at museums allow us to find these fossils that are sort of like still hidden back in our archives. And then the biggest thing I think is international cooperation and the ability to work with scientists from around the world like we did with the scientists in Dalian. So my old advisor, Dave Riccio and I, a now coworker, we actually have a specimen that we just got accepted to a paper, and I can only say so much, but it's going to tell us a lot about dinosaur reproduction. And so this is a dinosaur that's actually really closely associated with some eggs. And we're working on this with scientists at the Gejong Natural History Museum in Southern China. So I understand there are actually eggs inside this fossil. That's correct.

And we presented on this fossil in the past, but we've done a lot more work on it. We're actually able to sample the eggs themselves and determine where they came from and able to come some really neat conclusions. And so that's a really rare tree. But it highlights how well the preservation of many of these fossils is in China and the value of working with people from around the world. You say we're in the golden age of dinosaur discovery. Why is that? Have anything to do with younger scientists coming into the field? So I definitely think it does.

And not just younger scientists, but also scientists of, not just one gender and not just one nationality and not just one language. And so I think this opening up of science in general has started to make it into paleontology. I think that's only good.

Not only is it a joy to work with a broader group of people, but it opens up new ideas and new places to search. So I think that in and of itself would mean it's a golden age in paleontology. Additionally, this is a time when we're discovering more than we ever have before.

And I think those things are linked. So I always say the last five years of dinosaur discoveries have yielded more new species than any other five-year period in history. So who's paying for all of this? I always preach, follow the money. If you're finding more things,

there must be more people who want to find more things. So that's a good question. And paleontology is not well known for being the world's best funded field. We're talking about particle physics here. That's why I'm asking here. I mean, if you want to use your platform

to help us find more dinosaurs, we'd certainly appreciate it. I think there's been more funding in other countries. I think that the National Science Foundation and other things are really responsible for a lot of this. And you see that, I hope, reflected in a lot more open publishing and scientists being really willing to share their work as widely as we can. And it's not always possible, but when it is, I think that's a really positive development. A lot of new books coming out.

Steve Brissotti had a great book a few years ago. That book's excellent. Yeah, everybody should check that out. And there's always, you know, there's always interested in dinosaurs and always, I know, parenthetically. that you also study whales. I mean, that's a jump, is it? That's a stretch. It does seem like a bit of a jump.

Well, partly, I think, I hope people, I know that people love dinosaurs, because I love dinosaurs. They love whales also, don't they? Exactly. But for me, whales take a lot of the same boxes, and people might say, oh, there's just whales, they're alive now, you know?

But for me, dinosaurs are these incredible monsters, but they were real. And I think because you can see one and you can see a video of one, you might not realize it, But whales are definitely real monsters. And that doesn't mean that they're bad.

I don't mean monster in that sense. I mean, they're monstrous. They are different from what we expect. They're huge. I mean, the dinosaur we described is tiny. But of course, dinosaurs also include the largest things that ever walked on land. But they're outsized even by the blue whale that we have alive today. These are animals that have grown the single largest bone that has ever existed on Earth.

And that's the bottom with single jawbone of a blue whale. And where I'm at now in San Diego. Diego, we have some of the best collections of fossil whales anywhere in the world. And so it's really a treat to get to work on that. And ask some of these same questions. So if you're interested in how a dinosaur becomes a bird, I think it's really cool to think about how a walking, hoofed, carnivorous, deer-like animal becomes a whale. And those evolutionary transitions are just insane. We're going to have you back, Ashley, to talk about that more. I'd love that. Because that's great stuff. Actually, is a postdoctoral researcher at the San Diego Natural History Museum. Thank you for taking time to be with us today.

Of course, thanks so much. When we come back, why drug researchers are flouting a federal law that requires them to publicly report results coming up after the break. Stay with us. This is Science Friday. I'm Ira Plato. It takes a long time before a drug can make its way into your medicine cabinet. And there's a good reason for that. Researchers have to recruit human subjects for a clinical trial, then collect all the data and analyze the results. And all of that can take years to complete. But the end result could be a drug candidate that treats a rare disease or improves patients' lives with fewer side effects. Or it could result in a drug that doesn't have any effect on a disease or makes patient

worse or is an absolute failure. Currently, there are over 100,000 of these clinical drug trials happening in the U.S. that can be found listed on a website, clinical trials. dot go, a public-facing website where researchers are required by law to register all clinical trials and report the results. This ensures that either way, if a drug candidate fails or becomes the next big thing, the public is kept informed. Except to recent investigations of clinicaltrials. gov, reporting practices show that many researchers aren't posting, they are not posting their results on the site. In fact, up to 25% of clinical trials.com, reporting practices show that many researchers aren't posting, they are not posting their

results on the site. In fact, up to 25% of the studies never seem to have their results reported anywhere. Even worse, government agencies are not enforcing the law in ways they've promised, with heavy fines and threats to withhold funding from institutions that do not comply. What does this mean for safety of our drug trials? And why has the government done nothing to crack down on researchers breaking the law? Joining me to talk about this is Charles Pillar, a journalist who conducted one of the investigations of the Clinical Trial.gov for Science Magazine. He joins us by Skype. Welcome to Science Friday. Thanks very much. I were glad to be here.

Nice to have you. Dr. Deborah Zarin is part of the Multiregional Clinical Trial Center at the Brigham and Women's Hospital in Boston. Welcome to Science Friday. Thank you. Happy to be here. Nice to have you. Charles, you've investigated this for Science Magazine. Give us a picture of what you uncovered. Well, the picture is not very pretty. This is a law that requires the registration and reporting of drug and device trial results. And it's critical to evidence-based medicine and for a variety of other reasons, including honoring the contributions of volunteers who, at some personal risk, agree to be the test subjects for these trials. And what I found was that, although there has been some improvement by some organizations, particularly as it happens, large pharma companies over the last few years

in reporting the results of their trials, there's been a terrible deficit in that reporting by some of the leading academic organizations, some of the most eminent medical centers in the country. And one I'll just note in particular is MD Anderson Cancer Center. So this is obviously one of the most important. research organizations in the country well known for its work on immunotherapy and other kinds of cancer trials. And one of the former executives at MD Anderson, who was heading up their program, is now FDA commissioner at Stephen Hahn.

And they had a terrible record for reporting worse than many of the most important academic medical centers. the country. So I know from your reporting that about a third of 31.6% of completed trials have not had their results posted. That's right. And I want to make it clear that this is a very conservative look we did at Clinical Trials.gov reporting. When I say conservative, what I mean is that there are hundreds of thousands of trials that are registered on the site. But because of a variety of legal and regulatory changes over the years. There's really just a small percentage of those that are right now, according to the government, and when I said the government, I mean FDA and the National Institutes of Health, according to those two very important agencies that

regulate this system. Only a tiny fraction of those studies are legally reported to provide the results by about now. And when we took a look at this data, this was back in September, it was about 4,700 clinical trials that were really needed to report their results by that time. And as you say, of those, almost a third had not reported any data. And even worse part of the picture is that even among the ones that were reported, many of them were reported late far after the deadline. So in essence, delaying the time when doctors, patients, and other researchers can gain access to that information. Dr. Zarin, can you give us a history of this law? Why did we need this law? How come, you know, it took till 2007 to get it on the books? Sure, and let me make sure your listeners know that you mentioned my current position, but I was the director of Clinical Trials.gov from 2005 to 2013 to 2018.

So I was living this experience. It used to be that investigators, whether from a drug company or an academic, would do a clinical trial, they could decide whether, when, and how to report the results of those trials. So the way to report them was in the published literature, but nobody was looking to make sure that they were published. And we now know that many weren't published. For example, drug companies might have done, you know, nine or ten studies of a particular drug and only published the one that came out to their liking. Another story is that, you know, a drug company or an academic might conduct a trial and publish it, but distort what the original protocol said or how they conveyed what was done in the trial. And even though it was in the peer-reviewed literature,

the journal editors had no way to know that this wasn't true, because there was no other record about what the trial was or that it existed. Academic researchers, we now know, only published about half of the trials that they conducted, for whatever reasons they just didn't publish the trials. And the thing is that it used to be that people like Charles Pillar couldn't have done the public audit that he's done because there was no list of trials. So if they didn't publish, you didn't even know they existed. So Congress passed the law that's fondly known as Fadda, the Food and Drug Administration's Act, to rectify this problem for drug and device studies. And I just want to say, even though I agree with Charles that compliance is nowhere near what we wanted to be, it's had a huge impact. So trials are in general being registered, which is again why these kinds of public audits can be done

because we have a pretty good list of all the trials that are initiated. And over 40,000 sets of trial results are in clinical trials. And about half of those are results that aren't in the published literature. So there would be no other way of knowing those results without clinical trials. of. But that being said, it's completely unethical to do a trial and not report the results because the only reason that society lets us let's researchers experiment on their fellow humans is so that the results are made available for the medical community to use those results to inform either medical or scientific decisions. If those results aren't made available,

there was no justification for including people in that trial and that's an unethical situation. Well, let me, let's talk about the watchdog. Supposedly the government's supposed to be a watchdog on publishing these things and supposed to have fines and things for the people who don't publish them, Dr. Zaron. Why have we not seen a rash of justice come down on this? That's a really tough question. And again, I'm not the one in charge of enforcement. I suppose if I was, the picture would look quite different. So first, there was a long, wait until the final rule or the regulations were enacted and those took effect in 2017 because the regulations clarified all sorts of details about this very

complicated law and at that time as Charles mentioned in the article that he published the leaders of those organizations it was dr. Caleb at the FDA and Dr. Collins at NIH, Dr. Collins is still the head of NIH, made very strong statements that they were going to enforce and it's very disappointing to me that they haven't done any enforcement. I think there are probably many reasons for that, but I find it, you know, unacceptable. Let me ask Dr. Pillar. What reasons do you think there are for that? Thank you for that, elevating my status to being a doctor.

But yes, there are many reasons for it. According to both NIH and FDA, they believe in quote unquote voluntary compliance. They want to use moral persuasion. They want to urge trial investigators to do the right thing. Unfortunately, what we've seen is that over the last five years, that that method, while it has some limited effectiveness, is really not what moves the needle in getting people to do the right thing and report their results.

And I say this advisedly in part because I've been, writing investigations about this topic since 2015. And the first one I did was with STAT, the medical and biomedical research news website. And what we found was that the situation was even worse back then, back in 2015, that there was horrific record of trial reporting by all kinds of sponsors, both corporate and academic. And what we did for the first time is name names to talk about the institutions that were the worst lawbreakers, the ones who seemed to show the least care about presenting the data associated with these important trials. And what we found was that that did indeed have an impact.

There was an improvement in trial reporting. Now, it wasn't obviously not exclusively due to that sort of reporting. NIH's efforts have been heroic in trying to educate researchers on how to do this better. And I credit them as well. But I think what we know from experience is that naming and shaming the scoff laws often has the most serious impact on this in the absence of enforcement. So why isn't there enforcement? And it's really a perplexing question because the comments coming, as Deborah mentioned, and the comments coming from the heads of FDA in NIH in 2016,

when they announced this so-called final rule associated with this law, was meant to just put people in notice. You've got years to prepare for this, years to ensure that your studies are now being reported effectively. And so now, years later, we take a look, and they're not being reported. And NIH and FDA are essentially doing nothing to enforce the law. But some academic medical centers have stepped up, right, to be in line with the law.

Indeed, indeed. And that's very encouraging. Now, I don't want to paint too bleak a picture. Let's talk on the positive side for a moment. Institutions, like some of the major pharma companies, are following the letter of the law. In other words, for the most part, they're reporting all their results within the legal deadlines. some leading academic medical centers such as Memorial Sloan Kettering, Duke University, Johns Hopkins, who were poor performers.

When I last took a look at this issue a couple of years ago, they are now doing much better and for the most part are complying with the requirements of the law and the ethical requirements of reporting their results. But I think just to caution listeners for one moment about what it means in particular for the drug companies that seem to have a kind of perfect record in following the law. There are many loopholes in the law that allow entities that are working towards approval, FDA approval to put a drug on the market, to withhold trial information from the public. And those are meant generally to protect proprietary information, trade secrecy,

to prevent competitors from getting a leg up on them. And it's understandable that that would be protected for some time, but it's been found in other studies that a lot of times the drug companies never report the results of those trials to clinical trials.gov. So the only way to even learn what happened is to dig deep into the FDA drug approval packages, which are really well beyond the capacity or the ability of 99.9% of doctors, let alone patients in general public. Let me just break in and say, I'm Ira Plato. This is Science Friday from WNIC Studios. So even while they're reporting, you have to really dig in there to find them. You mentioned these drugs, and you singled out M.D. Anderson, very well-known Cancer Center in Houston. Are you naming and shaming them today?

Well, indeed, and in the article, some of the institutions that we think of as being the most, in the country. The most important progenitors of clinical research in the country, including M.D. Anderson, Mass General, Mayo Clinic, and others have had really mixed to terrible records in reporting their results. And one of the reasons I single some of those out, we'll just take M.D. Anderson as an example, they have the highest number of clinical trials due for reporting under the new so-called final rule that we looked at for this story more than any other institution. And I looked at their performance years ago, and I found that they actually did worse now than they did years ago in reporting the results of their

trials. So that's a pretty troubling piece of data. Let me break in and ask Dr. Zarin how she would think how you would incentivize academic medical centers to be more compliance? Well, that's a really good question. And, of course, I've thought a lot about it. You know, what you'd like is leadership to understand that reporting your results of your trials is both a scientific and an ethical imperative. And we don't see much of that.

Sometimes at academic medical centers, at least from their public statements, what you see is not wanting to be on the wall of shame. So you see them saying it's a law, you have to do it. which works, but isn't as good as saying, not only do you have to do it, but there's a really important reason that you have to do it. I like to compare it to the regulations that require that we get informed consent from every trial participant. Imagine if there was an academic medical center that had 80% compliance with that particular requirement. Would they be proud of that? Would society stand for the fact that 20% of their trial participants didn't even give informed

consent, and yet being in a trial that has no chance of advancing medical science is, to me, equally as unethical as not giving informed consent to be in a trial. So it's important to think about that. So without the leadership of your academic medical center caring about whether you do this other than whether you're going to get caught and shamed or worse yet, actually enforced, I think there needs to be both enforcement by our government agencies, FDA and NIH, and we need to people like Charles Pillar to keep holding people accountable. I think public accountability, which again is possible because in general people are registering their trials. You can get that list of trials from clinical trials.gov. Public accountability is probably where we have to go

and really make it very uncomfortable for institutions to be out of compliance. Well, we've given you a little platform to allow the public to know what's going on. I don't think this is something they were very much aware of and how much it impacts research. Thank you, Dr. Zarin. Deborah Zarin, part of the multi-regional clinical center at Brigham and Women's Hospital in Boston, and who was also part of the Clinical

Trials.gov organization, Charles Pillar investigative journalist for Science Magazine. Thank you both for taking time to be with us today. Thank you so much. Thanks, Ira. You're welcome. After the break, we're going to talk about

how chemistry might be the key ingredient to your perfect cup of coffee. We'll be talking about coffee science. Got a question. Do you have a question? Who doesn't about coffee science? 844-8255 is our number. You can also tweet us at SciFry. We'll be right back after this break.

This is Science Friday. I am I.Rof-Fledo. Is making your morning cup of coffee like a sacred ritual, carefully grinding the beans just a certain way, depending on if you're having an espresso or a drip? Next, you boil the water to the exact temperature, not too hot. And finally, you brew. Are you going to steep it, pour it over,

or leave it up to the coffee maker? There's a lot of details that go into coffee. But what is the science going on behind those steps? Because as we know, a dose of science can make most things better and your coffee more consistent. A team of researchers used math models to figure out the optimal grind size to get the most out of your espresso pole. The results were published in the journal Matter.

Christopher Hendon is one of the authors on that study, and an assistant professor of chemistry at the University of Oregon in Eugene. He's here to talk about these results and to talk coffee science, because we know the best part of waking up is having chemistry in your cup. Welcome to Science Friday. Hi, Ira, thanks for having me. I know you spend a live, read all these papers you've written. You spend a lot of time on coffee chemistry, don't you?

That's right. You know, I like to think of it as one of my more sophisticated scientific outreach programs. So I know you're working on building new kinds of materials, right? What does that have to do with coffee? Well, a lot of the chemical principles that I use in my day-to-day lab with my graduate students and undergraduates here at the University of Oregon are based on this or are an application of the same principles that we're using in the coffee science. What I study here at UO is related to energy materials and more often than not, in energy there is transfer of management. mass moving from one place in space to another. And you can actually think of that problem is the same problem when you're modeling or

thinking about how you extract coffee. Interesting. I want to get into the chemistry of coffee, so I'm going to give out the phone number. 844-8255. You can also tweet us at SciFRI. Let's get into the grind. Your study looked at getting a consistent shot out of your espresso pole. An espresso is right.

usually brewed with a very fine grind size, but you found something different. Right. So currently, the average way of producing espresso is to grind very, very fine and use something like 20 grams if you're in the United States, Australia, Germany, et cetera, and move about 40 to 50 milliliters of water through this 20 gram puck of coffee. On average, you're going to extract something like about 20% of the mass. So 80% of the mass is going to be wasteful, and that 20% of the mass is, ended up salivated in the cup and hopefully tastes good to you as the end user.

When we were examining building a model, we thought, well, okay, the extraction must be related to the surface area available from grinding the coffee. And so as we developed our model, we realized that as you grind finer, you expose more surface area. And so one would then expect for the same amount of coffee and the same amount of water that you should be able to extract more proportional to the surface area. But in reality, we found that actually grinders produce very small particles and relatively large ones as well. And these two particle sizes coexist. And when you produce a critical number of these small particulates, they tend to clump. Now, at certain grind settings, sufficiently fine. You'll find that the clumping actually causes

the water to percolate through that bed in an in homogeneous or uneven way. And it is at these grind settings that we also happen to find are widely used in the production of espresso. And so the conclusion from the, or at least when examining the status quo is that conventional espresso today is used with an uneven exposure of the coffee to water, resulting in variation in flavors that are not attributed to the human, but rather attributed to the method in which we produce espresso right now. All right. Let's say I want to make my own espresso, or I just want to do it in the coffee maker.

How do I decide what's the best grind for me? Because I can go to the supermarket and grind it to different consistencies. That's right. What can I do at home to make sure I'm getting the best grind? And how do I experiment with that? That's right. So this is sort of touching on a flavor perception problem as well. So typically we would advise to start with coarsely ground coffee.

And now by and large, when I mean course here, I don't mean French press course. I still mean an espresso grind. and it's still quite fine to you, the human eye. You start grinding with that dose, and you're going to brew some of coffee. And if it tastes a little thin and a little weak and perhaps a little too acidic and not enough chocolate, then you want to grind a little finer. And now you're going to progress doing this to a point. But at some point, you're going to notice that the concentration of the coffee,

in other words, the strength is beginning to decrease, and the flavor intensity is beginning to increase in a negative way. And at this point, you know you've gone over the hill, and you're no longer evenly extracting from your coffee, you're in the side of uneven or in homogeneous extraction, and you need to back off from there. Once you're at that point, that's where the real fun begins. Wow, that's great.

I can experiment with that because I'm a geek and I can become a coffee geek, I think. One thing I've heard controversially over the years, and we've talked coffee for almost 30 years around Science Friday, is people have different opinions about how to best store their coffee. Right. In the freezer, in the refrigerator, in on the counter. What have you found? So actually in 2016, I actually studied this and we published that in an open access journal. One of the key things with coffee is that it begins its life as a seed

from a plant. So it has about 11.5% moisture contained within. And once you roast it, you're going to drive off almost all of that water, if not entirely all of it, make it completely anhydrous. And so obviously this material is going to be much more dry than the atmosphere that it's surrounded by. And so it's going to want to condense water within. So the first and most important thing is to make sure that you keep the coffee air-free, but only because you're trying to keep away water or moisture. However, we're then put in a bit of a pickle because the erroneous equation tells me that if I cool things down, most rates of reactions go slower.

So if I want to preserve coffee for a long time, I want to keep it as cool as possible, perhaps in the freezer. But the problem with a freezer, of course, is it's pretty wet. So you're stuck in this sort of in the middle here, a push-pull. And so what we actually end up recommending people do is to keep it in the freezer but in a vacuum-sealed type vessel. You see this occurring more and more. And at the moment, we don't have a polymer, the type of plastic bag perhaps that you would be able to reuse. So it's somewhat wasteful at the moment. And so therefore you only see this in very special cases where you're trying to preserve very high-value types of coffee.

Why couldn't I put it in a jar and put the lid on time? That works perfectly fine. But if you open up the jar while the coffee is still cold, in the room in the atmosphere, then you're going to condense water from the atmosphere onto the surface and inside those beans. And so the more times you do that,

progressively you're going to have more and more water being condensed within that vessel. That's freezer burn. Indeed, it is freezer burn, yeah. And you don't want your coffee is smelling like fish sticks. That's true. Now, when I take the coffee out to grind it, do I grind it frozen?

I want to grind it frozen that way? So we've actually found that temperature does directly affect the size of the smallest particles in the grind. And it happens to be favorable. So actually, as you cool down, cracks propagate through materials more quickly and result in more unified particle sizes. And so these small particulates actually are formed and are very reproducible when we cool this coffee or cool any material for that matter.

And so we do recommend actually grinding it frozen. and then once you expose the frozen grounds to hot water, they very quickly equilibrate to the temperature of the water. And brewing is as poor normal. All right, let me get to the water because I found something amazing in your research, and that is we should not be using distilled water, reverse osmosis, whatever.

We should be using hard water when making coffee. Yeah. So this language of soft and hard is complicated because it's very easy to define soft. you know, water that doesn't have very many minerals dissolved within. But hard water is simply defined as water that contains lots of minerals, but it depends on their identity. So instead of talking about calcium and magnesium, and they are important, the main mineral we're trying to avoid using is bicarbonate, because bicarbonate creates a buffer to try and

stabilize the pH, and coffee itself is acidic. In fact, we like the acids in coffee, even if we don't perceive them necessarily as, you know, the peel of a lemon or whatever, we still enjoy the acids because they taste like sweetness and acidity. So we simply don't want to use water that contains high levels of bicarbonate, but if we could have other minerals there that did not buffer acids, then that would be ideal. Does a water softener have bicarbonate in it? So typically a water softener actually is exchanging out calcium and putting in sodium. And so why it's softening the water is it's preventing calcium and carbonate. to coexist forming lime scale.

But it's not actually killing the bicarbonate. It's simply actually removing the thing that we actually want for coffee extraction, which is calcium. Wow. I'm just, you know, because I always thought the pure of the water. So, well, let me go back to that. Does that mean, you know, we here in New York, we talk about, we take our coffee seriously, we take our bagels seriously? Very.

I mean, could that be the same kind of watery thing going on and what makes a bagel better than what makes one coffee better. Interestingly, there is a company that has re-created the chemistry of New York water for making bagels. So people have caught onto this idea already. The reason that we were talking, and you first mentioned, the idea of using soft or distilled water as being a positive thing for coffee, is not because it's somehow, you know, that's what's taught. It's not because it's somehow better or worse. It's because it doesn't have bicarbonated it.

That's just a guarantee. So at least you know you're going to get some of the positive flavors out. But when you're looking at New York tap water or municipal water provided wherever in the state of New York, you're right. It does impart some sort of terois, some chemistry related to New York's specific water. And that has enabled the production of things like bagels and exceptional coffee in the city. See, you've just justified what we like to say here in New York. Thank you for that. Yeah, you're welcome.

Okay, let's go back to brewing methods now. I'm going to move through because there's a lot of interesting things. There's a trend now at coffee shops where you can choose your brew method, right? You're pour over, you're steeping. How do these methods extract the coffee molecules out differently? And how do you choose which one is right? Yeah, that's extremely complicated. So shops that offer a wide variety of brew methods are really working hard to present that as an option for the customer.

More often than not, you'll find maybe one or two choices. for a given coffee. Typically, baristas, shop owners, roasters, home enthusiasts are making decisions about how they're going to extract that coffee based on primarily three things. First of all is the roast degree. So it is typical in the coffee industry to find darker roasted coffee being used in espresso. And the reason is, is that you are going to sort of moderate some of the acids that exist in the green bean so that you're not going to get something that's extremely acidic and very hard to enjoy. And so you find the dark roasted coffee are more prevalent, and that pretty much summarizes the Seattle coffee scene at places like Italy and so forth. The next thing

that practitioners typically want to consider is the concentration in which they want to consume the coffee. So if you make a filter coffee, you're going to use 20 grams of coffee, say, but you might then pour over 250 milliliters of water on it. And that makes a much more dilute beverage than if you were to use 20 grams of coffee and use only 40 milliliters in an espresso machine. And so indeed, it is coffee specific as to whether you want to taste the concentrate or the stretched out version. Let me just remind everybody while we're having our next cup of coffee, I'm Ira Plato. This is Science Friday from WNYC Studios. Talking with Christopher Hendon, assistant professor of chemistry at the University of Oregon and Eugene. Would you be a coffee geek?

Would that be the correct classification or coffee enthusiasts? I think now I'm a a coffee researcher. Oh, okay. Yeah. Do you have your favorite method of a brewing, brewing method that you use? Yeah, so in my office, when we have academic visitors, I love to present them a coffee that has unusual flavors and so forth. But I typically find the most reproducible way for me to do that in my hands is a pourover

method, something like a V-60 or a Kalita wave or something like this. But if I were to go out and enjoy a coffee, by far my favorite format, is that you. is to try the coffee both as an espresso and with espresso with a little bit of milk. And I call that a one-in-one, where you have the same shot split in half. That way you know you're getting the same espresso, but you can see how the flavors translate when you add milk. Isn't that called Cafe Ole in France? The Cafe Ole is indeed, yeah, you're right.

It's a coffee plus milk, but probably a bit bigger than the old espresso and cortado combo I'm talking about. I remember growing up with a percolator. Oh, yeah. How does that work differently than the way we brew coffee now? So it's interestingly, it's becoming more popular once again. There's been a resurgence in the percolator. Yeah, it's bad. Going into my basement.

Yeah, well, yeah, it's probably worth a lot of money now. The inventor actually recently passed away, and there was a big ceremony in Italy for this. It was, you know, it was essentially a party because indeed the percolator was sort of one of the earliest embodiments of the portable espresso machine. in the sense that you start with water at the bottom, you boil it, you create a critical pressure of steam, and that steam pressure that is then forced through the puck of coffee, that gives you an extraction that is only enabled by having that addition of pressure, and then you can get a very concentrated beverage out of it. And so actually a percolator is essentially a portable espresso machine without all the bells and whistles. Yeah, but it also recycles the coffee over and over again, doesn't it?

Goes through the basket, goes back up again. Yeah, there is a little. So it depends on the design. Of course, there's ones that look like a fractional distillation column where once the water is sufficiently boiled and steam passes through the puck, it then goes through this sort of cap and can no longer recirculate. So it depends on the embodiment, but you're right. That's the vacuum one, is it? With the big bowl on the top and the pot on the bottom goes up through?

Yeah, so I think the one I'm referring to specifically is sometimes we're called the mocha pot. And the percolator coffee is does have this. It's more or less a mocha pot. with a recycling feature. But, you know, either of them are having a resurgence because of its portability. So it really is. It's not the machine we think it is. Something a little more complex.

That's right. And, you know, just for someone who grew up with a percolator as a teenager, is something also, it helps your body. You feel good when a big pot of coffee comes over, you know. It's the experience that you don't get from a little pourover or in a cone. I'm sorry. Yeah, so in the percolator sense, you're thinking, in this case, we're referring to like a Mr. Coffee type product, one of these big pots that you find at the, oh, I see. So when I think of the percolator, I was referring more than mocha pot. I'm sorry. No, no, I'm talking about the percolator that, you know, is the stainless steel thing you plug into the wall. Yeah.

That's the one I'm referring to. Yeah, yeah. So you're right. You know, there is something that still, you know, it still resonates with me as well. And I go into a diner, for example, and I see this big pot of coffee sitting on top of the brewer. And, you know, it means it's going to be a good day. I'm going to end it there because that's my cup of coffee also. That's the coffee kind of coffee I like. Thank you very much, Christopher. My pleasure.

Absolutely enlightening us about coffee and everything we needed to know. Christopher Hendon, assistant professor of chemistry at the University of Oregon and Eugene. Just a quick note, our Science Friday Vox Pop app, we'd like you to go there for our next degree of degrees of change series. we're looking at how climate change is affecting Native American communities. If you are a tribal member, we want to hear what adaptations you and your community are making. And please go there and tell us how it's affecting your tribal community and leave us a message. And maybe we'll play you back on Science Friday next time we do our degrees of change series. Also, we're on social media all week long and say hello to us there.

And hope you enjoyed the show today. I hope you were able to listen to it by, you know, tell us how you were able to listen to it. Were you able to listen to it live on the live feed? We'd like to know that. Have a great weekend. I'm Ira Flato in New York.