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Displaying results 80401 - 80450 of 87950
Teaching Synthetic Biology
I recently found this fascinating (relatively) old review article (open access) by awesome MIT professor Natalie Kuldell about teaching synthetic biology. Synthetic biology has integrated teaching and learning with the development of the field since basically the beginning of the field, with students contributing to new technologies through iGEM and academic lab-based courses. By actively participating in a new field students get a unique educational experience, and the field benefits through the work of students being trained as engineers and biologists: Synthetic biology, with its inclusive…
Lott's letter campaign continues
Another letter has been sent to the Washington Post, and by an amazing coincidence makes the same error about the Post article as the previous ones: A column appearing in the Post yesterday (Feb. 11, "Fabricated Fan and Many Doubts") implies that economist John Lott made up the claim that a computer malfunction destroyed data from his research on gun control. At the time Lott was engaged in this research, we were colleagues at the University of Chicago Law School. I clearly recall John relating the computer data-loss incident to me then---many years before the current controversy…
Bacterial Buddies
Commenter JohnV asked me whether I had let any of my silkworms crawl on an LB plate (what microbiologists use to grow colonies of bacteria) to see what kind of bacteria is living on them in case I ever suffer from catastrophic experiment contamination. I hadn't thought of what kind of bacteria could be living on my silkworms (we are thinking about what kind of bacteria live in their digestive systems that help them digest leaves) so I tried it out! I let one of my wormies crawl on a plate, and I touched one with my relatively clean fingers as a pseudo-control. I let the plates incubate at 37…
Non-Science Fridays: ERs are almost worthless
Don't go to the ER. So yesterday I was excersizing relatively strenously and after about 40 minutes I started to have some chest pain on the left side along with tightness in my neck and shoulder. Hmmm...good time to stop. It wasn't really severe so I took a shower but the tightness and some pain remained but decided to head home as it was likely just some pectoral strain. Then I realized that if I heard about me, I'd call me stupid so I thought I should go to the hospital just in case. Well, that was the dumb idea. I was directed to an urgent care: "You'll get seen right away, but in ER,…
Stupidity about cancer and meat
There's a story in the WashPost today about how spicy marinades decrease the heterocyclic amine (HCA) content in grilled meat. They think you should care because HCAs are likely carcinogens. There are many things about this that get my back up so lets make a list: 1) Nobody knows how much cancer HCAs may be causing. As far as I can tell (I'd be glad to be e-mailed some reasearch that disputes this), there isn't any study that directly links HCAs to human cancer, qualitatively or quantitatively. I'm not saying they're not carcinogens, I'm pretty certian they are, but the only studies that I…
Details on the future of the deCODEme service
I was just sent this email by a deCODEme customer: As a valued subscriber to deCODEme, we wanted to write to you directly to let you know about some important developments in the company and how we believe these will underpin our ability to continue to keep you in the forefront of understanding what the latest advances in genetics mean to you. For the past several months, deCODE has been working on restructuring its operations. One of the principal goals of this effort has been to enable us to find new investment that will continue our work in human genetics and to offer to our customers…
What is it with rich white guys and genome sequences?
David Dooling has an entertaining take on the Helicos genome sequence I discussed yesterday entitled "Another rich white guy sequences own genome". I noted in my post yesterday that the alleged price drop for the Helicos sequence over current technologies was an illusion, but David includes a much more thorough analysis of the relative genome sequencing costs thrown around over the last couple of days and makes it very clear that the price Helicos is quoting is really no advance over the current prices for second-generation sequencing technologies: They report reagent costs that are on par…
Memories: trust provisionally, but verify always
Steven Novella makes an important point: memories are fluid. There's no VCR in your head, and no tape recorder either, and memories are constructs. You remember the framework (sometimes very poorly) of a past event, and your brain builds a plausible set of details around it. When you picture Christmas at your grandmother's house when you were 12, you don't have a record in your head of how many logs were in the fireplace or a second by second recording of the flickering of the fire. You remember that Grandma had a fireplace, and sometimes she had logs burning in it, and maybe there was a fire…
LA Times Article about Pro-Test UCLA founder David Jentsch
The LA Times has an article today about the founder of the UCLA chapter of Pro-Test, David Jentsch, a neuroscientist whose car was torched last month by animal rights extremist. This point is particularly relevant: "People always say: 'Don't respond. If you respond, that will give [the attackers] credibility,' " Jentsch, 37, said in a recent interview in his UCLA office. "But being silent wasn't making us feel safer. And it's a moot point if they are coming to burn your car anyway, whether you give them credibility or not." Jentsch is right. The lesson of Pro-Test Oxford was that silence…
Do You Blog About Peer-Reviewed Research?
If so, you'll be interested in today's announcement from BPR3 (Bloggers for Peer-Reviewed Research Reporting): We're pleased to announce that BPR3's Blogging on Peer Reviewed Research icons are now ready to go! Anyone can use these icons to show when they're making a serious post about peer-reviewed research, rather than just linking to a news article or press release. Within a month, these blog posts will also be aggregated here, so everyone can go to one place to locate the most serious, thoughtful analysis and commentary on the web. But we encourage you to start using the icons now. They'…
HPV Vaccination in the New England Journal of Medicine
This week's New England Journal of Medicine is a virtual smorgasbord of articles on HPV (human papilloma virus) vaccination. Although HPV also causes unsightly genital warts, HPV is more or less the sole cause of cervical cancer. I've written quite a bit here about Merck's HPV vaccine, Gardasil, since a February 2007 executive order by Texas governor Rick Perry made the vaccine mandatory for sixth grade girls in the state but was subsequently overturned by the state legislature (and Perry announced just this Tuesday that he would not veto the bill, which had been passed by a veto-proof…
Ask a ScienceBlogger: The Nuclear Test Ban Treaty as a Science Policy Success
This week's Ask a ScienceBlogger question is "What are some unsung successes that have occurred as a result of using science to guide policy?" I think there are several good answers to this question, including several successes in basic science (the NIH, basic science funding), health (vaccination, AIDS relief), space (NASA, the Hubble Telescope), and environmental (the formation of the EPA, the Kyoto Treaty) policy. One success that might not be so obvious, though, was the Partial Test Ban Treaty (PTBT). When it was signed and ratified in 1963 by 113 countries, including almost all of the…
Inquiring Readers Want to Know: "Why is My Poop Green?"
Photo source, San Jose Library Flickr Photostream. So you're on ScienceBlogs. What interests you, what are you looking for? As a regular blogger, I wanted to know. One way to explore these questions is to take a random sampling of keywords that readers have used to search this site. I selected the past month and scanned the top 500 terms (out of a total of 292,566 - but who's counting?) During this past month, there were 3,860,385 visits at ScienceBlogs. I learned something interesting. Take a look at some of my favorites, listed below and ranked from high to low popularity: {I may…
Diabetes: Red Wine or a Pill? You choose.
Source. Prescription medications for the management of type 2 diabetes, while effective for many patients, have been fraught with side effects including weight gain that can make the disease worse given its link with obesity. Would it be possible to replace the pill with natural alternatives? Diet and exercise has long been known to be a highly effective method to manage type 2 diabetes, giving some patients more benefit than typical prescription medications. Since the discovery of the "French paradox" in the early 1990's that noted a low incidence of heart disease in France despite diets…
Unique Global Carbon Footprints
For atmospheric carbon dioxide levels to stabilize, this chart clearly shows, the world's major emitters and smaller countries will have to reduce emissions. If you've ever wondered about how each nation contributes to the global carbon "footprint," take a look at this compelling graphic. The left "footprint" displays recent data from the U.S. Energy Information Administration. The size of each circle - in some cases a "heel" or a "toe," is proportional to the carbon emissions estimated for each nation. The right "footprint" shows the same data, but expressed per capita so that you can…
A New Ruler for Learning?
. Photo by cohdra (source) What is learning? Is it the ability to recall facts or to solve an equation? How can you measure it? For college bound students, the Advanced Placement (AP) exam has attempted to address these questions since 1955 and offers students an opportunity to earn college credit while attending high school. A major portion of AP exams includes multiple choice questions along with a free response section. As a student, I disliked multiple choice questions because I would often second guess myself. What if the "obvious" answer is a trap? In contrast, the free response…
Homeopaths meet tomorrow for "AIDS" conference
On June 6, a group of deluded and dangerous people will meet to discuss how their brand of magic can heal the sick in developing countries. The Homeopathy for Developing Countries Conference in Amersfoort, Netherlands will bring together quacks and misguided "healers" to immerse themselves in solipsistic self-congratulation whilst promoting a mysticism that could spell death for hundreds of the world's poorest people, if not more. They say: Some homeopaths have even decided to permanently live in Africa or another region where medical help is scarce. These people do wonderful work because…
Eyes closed tight
You might have wondered, like I did, how Ken Ham was going to deal with the revelation that his prize Allosaurus specimen was the gift of a freaky neo-Confederate crank. We now know: he's going to ignore it indignantly. Rachel Maddow had a segment on the allosaur, the creationists, and the neo-Confederate. She makes some good points: why is this kook being given tax incentives to build another pile of bullshit in the state of Kentucky? How can they claim that this ancient fossil supports their claim of a young earth? And what about Michael Peroutka? Watch it yourself and see.…
The Nature of Authorship
A letter to Nature published this week asks when journals will begin to allow multiple last, or senior, authors. The letter is short, sweet, and to the point: The correspondence mentioned in this letter wonders how the author list should be organized: I thought I understood the guidelines for determining scientific authorship: the individual making the greatest intellectual contribution is the lead author, followed sequentially by those making progressively lesser contributions. In addition, the final-author slot is sometimes reserved for a lab head or project initiator, who may have made…
Bad Article on Genetics Blogging
Nature Reviews Genetics has published a terrible review of genetics blogging. And it's not just because they don't link to yours truly. The author links to Alex and Paul Zed, which means she knows about the ScienceBlogs empire network. I guess she didn't poke around long enough to find evolgen or Gene Expression. Maybe she saw them and wasn't sure if they were genetics blogs; it's not like the names give them away. The article sucks for the most part because it's an exercise in shoddy research. The author attributes Mendel's Garden to Hsien-Hsien Lei. Hsien hosted the second edition, but the…
You Got a Fast Gene
David Haussler and colleagues have identified a 118 base pair sequence that has evolved really fast along the human lineage relative to the chimpanzee lineage (Carl Zimmer has a good review). In fact, this sequence differs by two base pairs out of 118 between chimpanzees and chickens, and 18 out of 118 between chimps and humans. Differences in relative rates usually indicate changes in selection regimes along at least one lineage. These changes could be due to increased selective constraint along one lineage, relaxed constraint, or adaptive evolution. More on that later. Also interesting is…
Good News about the NIH Budget
President Bush's FY2007 budget included no increase in funding for the NIH. Scientists have been lobbying Congress to amend the budget to at least increase the NIH budget to keep even with inflation. You can follow the story in these posts: Lobbying the Senate Amendment passes in the Senate Lobbying the House of Representatives Amendment fails to pass in the House Budget Committee I just got word that the House of Representatives passed the FY2007 Budget Resolution which includes an amendment that ensures that all programs within the Labor, Health and Human Services and Education…
Speciation Blogging
There's lots of cool stuff coming out in the speciation literature. The Questionable Authority has posted on two recent studies on sympatric speciation (see here and here). Nature, which published the two sympatric speciation papers, has a summary available here. I am of the opinion that most examples of sympatric speciation are actually allopatry with reinforcement (for more on this, see here). That is not to say that sympatric speciation is impossible, just extremely rare. In the end, some reproductive isolation is a requirement for speciation in sexually reproducing organisms (whether…
Evolution, Development, and a Misphrased Question
To be filed under: You keep using that word. I do not think it means what you think it means. My name is not Inigo Montoya. You did not kill my father. And I couldn't care less if you died or not. But give me a god damn break here people. If you want to ask a question, then ask the question. There is no reason to not ask the question. What question am I talking about? As Chris and John have pointed out, the Brits ain't down with evolution. According to the BBC: "More than half the British population does not accept the theory of evolution, according to a survey. "Furthermore, more…
Expelled Exaggerated?
The creationist movie that everyone* is talking about came out was released this weekend. Early reports have Expelled coming in 9th nationally in weekend gross, with about $3 million. That's a lot of money, and you can color Randy Olson freakin' impressed. However, put in the context of what the producers were expecting, it's not so good. That doesn't stop Randy from pulling at Matt Nisbet and touting how awesome the creationists are and how shitty the "evolutionists" are. Fucking "evolutionists"! I'm gonna go off on a rant here, but, before I do, allow me to point out the beautiful irony…
A Question about Retroposition
Duplicated genes can arise via various mechanisms -- polyploidization, chromosomal duplication, segmental duplication, and retroposition -- and we can usually distinguish the various mechanisms as each has distinct signatures. For example, retroposed duplicates arise when an RNA transcript is reverse transcribed back into DNA and re-inserted into the genome. This is how many transposable elements (TEs) and viruses propagate throughout genomes, but the reverse transcriptase encoded by TE and viral genomes can be used on endogenous transcripts as well. Because they arise via the reverse…
JUNK RAFT Days Away from Hawaii!
Now it's time to share the truth. Back in the first week of June the Junk Raft expedition faced some very dark days. When they were first towed out to the Channel Islands one of the pontoons broke apart, forcing them to stop and gather the plastic bottles that came loose. Then, a day later they discovered the lids of almost 1000 of the bottles were working themselves off, filling the bottles with water, causing the raft to slowly sink. When Anna Cummins took a repair crew out to San Nicholas Island she told me the raft was basically sinking and would have been done in a day or so. How…
I built a microscope today
I did! It was an origami microscope, with a single simple lens added. Here's what it looks like: It's called a Foldscope, and I got it as part of a beta test program. It's a bit like the original Leeuwenhoek microscope, which you held up to your eye to see a magnified image. The differences are that Leeuwenhoek used a drop of water to form a spherical lens; this comes equipped with a pre-printed lens. Leeuwenhoek used brass and little thumbscrews to move the specimen around; Foldscope comes on a sheet of thick paper, and you punch it out and fold it, and then move a slide around under the…
Yet another one in the annals of inadvertently revealing anti-vaccine views
Time and time again, anti-vaccine activists respond to charges of being "anti-vaccine" with a self-righteous wounded whine that goes something like this: "We aren't 'anti-vaccine.' We're pro-safe vaccine." Alternative claims are that they are "vaccine safety watchdogs" and that they'd vaccinate if only the government would "green our vaccines" or "space them out" or that they think the government isn't listening to them or whatever. Of course, all of these are smokescreens for their true agenda, which, at least among the activists, is anti-vaccine to the core. In fact, so engrained are anti-…
Scientists Reinvent The Plant
Carbon is cycled from gas (C02) to solid (plant tissue) and and back (through fire, digestion, fermentation, etc.) again and again. Some of that carbon is trapped over long periods in the form of "fossil fuels." The earth has, in a sense, grown accustom to having a huge chunk of the available carbon stored away in coal and oil, so the recent (last century or so) release of large quantities of this carbon is a problem. This is why fuels made of plants (ethanol, diesel) are of interest. But those fuels require two steps: The carbon is captured by plants, then the plant matter is converted…
Every Culture Has A ....
... has a what!?!? I don't know how many times I've heard the phrase "Every culture has a story about a flood..." This is very annoying because a) it is not true (I can think of several cultures that do not) and b) it is very Euro-centric, as are most phrases that start with "Every culture has a..." So, I decided to enter the phrase "Every culture has a" into Google and see how many other stupid ideas I could find. The list is not very long because this exercise, while interestring in principle, can get a bit old. But here is what I found before I tired of it: Every culture has a folk…
Bees Teach Techies a Trick or Two
You all know about the honey bee waggle dance. A bee finds some nectar, returns to the hive, does a dance that communicates information about where the nectar can be found to other bees, and off the workers go to get the nectar. Techies at Georgia Tech have applied this method to developing a better way to run servers. After studying the efficiency of honeybees, Craig Tovey, a professor in the H. Milton Stewart School of Industrial and Systems Engineering at Georgia Tech, realized through conversations with Sunil Nakrani, a computer science colleague visiting from the University of…
Tomas: Good news and bad news.
Tomas is nicely demonstrating the degree to which meteorological models depend on the context of experience. This season I've read most of the discussions and advisories for most of the Atlantic storms, and generally speaking, the forecasts change only a little from time to time once a storm is named, and the final realized path and strength changes match very closely with with was predicted. Occasionally a storm is more poorly behaved than that. But Tomas, which formed in a place no other storms formed this year and that has existed under rather unusual conditions is giving the Hurricane…
A Case for Limits on File Names
Ray Ingles pointed out this position paper which I think is worth looking at ... Traditionally, Unix/Linux/POSIX pathnames and filenames can be almost any sequence of bytes. A pathname lets you select a particular file, and may include one or more "/" characters. Each pathname component (separated by "/") is a filename; filenames cannot contain "/". Neither filenames nor pathnames can contain the ASCII NUL character (\0), because that is the terminator. This lack of limitations is flexible, but it also creates a legion of unnecessary problems. In particular, this lack of limitations makes it…
James Randi and Global Warming
Yesterday, James Randi put up a blog post in which he questioned the validity of anthropogenic global warming. He has subsequently made the statement that he probably has more thinking to do about global warming, and he admits that he really knows nothing about it. So Randi's blog post is, essentially, a non-starter as an issue, although there are some interesting things to think about. James Hrynyshyn has an excellent blog post about this, in which he reports a conversation he had with Randi about Randi's post. Randi's original post displays a rather embarrassing ignorance of earth…
Every Culture Has A ....
... has a what!?!? A rewritten repost for your amusement I don't know how many times I've heard the phrase "Every culture has a story about a flood..." This is very annoying because a) it is not true (I can think of several cultures that do not) and b) it is very Euro-centric, as are most phrases that start with "Every culture has a..." So, I decided to enter the phrase "Every culture has a" into Google and see how many other stupid ideas I could find. The list is not very long because this exercise, while interesting in principle, can get a bit old. But here is what I found before I…
A strange night
It is a strange night. It is always strange when the water softener is recycling, because it makes all sorts of strange noises, and I usually don't hear them because I'm in bed sleeping. The BBC is being strange. They have a story that actually says: "Black bears are often considered among the most dangerous animals in North America, depicted down the years as ferocious predators threatening to man. But, says one man, that perception could not be further from the truth. " No, sorry BBC. We who live among the bears don't think this. Moose are far more dangerous than black bears and we…
Will Minnesota Standards Allow Creationism in the Classroom?
The following story is current, but the issue is not new. But interesting. ... Science standards for Minnesota schools are about to be set for the next six years. Is the battle to keep pseudoscience out of our classrooms over? Sadly the door has been cracked open for intelligent design, an idea with no real scientific basis cooked up by creationists, to remain in Minnesota's classrooms. The same vague science benchmark that was a compromise in the intelligent design controversy early in the Pawlenty administration still exists, unchanged, in this round of science standards. These standards…
Thanks to all...
Thanks to everyone for your kind comments about the recent bad news about our dog. (Even someone who really detests me because of my position on the vaccine/autism issue was in this instance kind.) I don't know if I'll feel much like blogging for a while; on the other hand, blogging has been therapeutic for me in the past when bad things happen, even if I don't actually write about them. It's always been a good way to take my mind off of badness by concentrating on other badness, such as quackery. Also, Echo has often been my little (OK, well, not so little) black blog buddy, lying nearby or…
"Green Our Vaccines": Best comment EVAH! Or: How to preserve biological diversity through not vaccinating
Maybe I need to inaugurate some sort of monthly award for the best comment, as some other ScienceBloggers do. If I had such an award, surely this comment earlier today by Prometheus would be in serious contention for it: Re: "Green Vaccines" One of the things that the "Greens" are in favor of is biological diversity and protecting endangered species. This dovetails nicely with the "Green Vaccine" movement, since it is clear to me that they (the "Vaccine Greens") are simply trying to prevent the loss of valuable biological diversity. Not too long ago, in 1977, one viral species (Variola or "…
On the Road Again: The Skeptics' Circle, a possible meetup, and Other Administrativia
In a couple of hours, I'll be en route to my favorite city in the world, a place where, although I lived there for but a brief three years, I felt completely at home. Chicago, baby! Yes, I'm on the way to the American Society of Clinical Oncology (ASCO) meeting in Chicago. While there, I'll be checking out the latest and greatest findings from the world of cancer therapy. As any blogger would, I'm hoping not just to learn something but to find interesting blog material. In the meantime, don't forget that the 88th Meeting of the Skeptics' Circle is fast approaching on Thursday, June 5 at…
Don't believe everything you see on a graph
This graph that Brendan Nyhan posted the other day got some attention from my coblogger John Sides and others. For example, Kevin Drum describes the chart as "pretty cool" and writes, "I think I'm more interested in the placement of senators themselves. Democrats are almost all bunched into a single grouping, with only four outliers. Republicans, by contrast, are spread through considerably more space on both the economic and social dimensions." Matthew Yglesias also labels the chart as "cool" and answers Drum by describing the pattern as "an illustration of the importance of setting the…
Chemistry confessions
I've just started my book tour for The Poisoner's Handbook and people seem to be wondering why I (a friendly mother-of-two) am so fascinated by poisons. I admit to a fascination with murder mysteries (count on me later in this blog to write about Agatha Christie). I share my affection for forensic dramas on television. I talk about the thrill of discovering two forgotten and quite heroic forensic scientists from jazz-age New York. And then I confess that I love chemistry - the most beautiful, the most fundamental, and on occasion the most sinister of all sciences - and that I even…
Looking somewhere other than under the streetlamp
Perhaps shockingly, I don't plan to so much as try to wade through all seven-hundred-odd pages of this report on scholarly-publishing practices. It's thorough, it's well-documented, it's decently-written… and based on the executive summary (itself weighing in at a hefty 20 pages), it won't tell me a thing I don't already know. Academia is conservative. Academia thinks its current scholarly-production system is just fine and dandy, thank you. Academia has a love-hate relationship with peer review. Academia wants to outsource its tenure and promotion decisions any way that is convenient and…
The dreaded backfile
One of the problems practically every nascent data-curation effort will have to deal with is what serials librarians call the backfile, though the rest of us use the blunter word backlog. There's a lot of digital data (let's not even think about the analog for now) from old projects hanging around institutions. My institution. Your institution. Any institution. There may be wonderful data in there, but chances are they're in terrible condition: disorganized, poorly described if described at all, on perishable (and very possibly perished) physical media. This pile of mostly-undifferentiated…
Animal Magnetism
No, we are not talking about mating habits here. We are talking about the ability of some animals to use the Earth's magnetic field to navigate and in the case of foxes, to find prey. In a recent article published in New Scientist, foxes have been identified as the first animal believed to use the Earth's magnetic field for more than simply determining which direction they are heading. While Dr. Hynek Burda from the University of Duisburg-Essen, Germany was observing the animals, he noticed that when the prey was hidden, the foxes almost always jumped on their prey in a northeast direction…
Sled Dogs and Diabetes
I recently wrote about how incredibly athletic sled dogs are, and given the recent weather forecasts for snow around the nation, I decided why not continue? Today, I'll focus on how similar the physiology of sled dogs is to human physiology (answer: extremely similar), and how this could possibly help two very different kinds of people - athletes and diabetics. In this video, Dr. Michael Davis of the American College of Veterinary Internal Medicine is interviewed by Steve Dale about the capacity of a sled dog's physiology to adapt to extreme stress. He says sled dogs are the greatest…
Snorkeling Elephants and an Introduction
This is my first blog, so bear with me. I asked a friend of mine how I should begin it, and he said, "tell them why they should care about what you will write about." Fair enough. I teach at a major university in the west. My area of specialty is the comparative physiology of glucose and fatty acid regulation. I specialize in this area because diabetes is such a prevalent concern in the United States. I accepted the invitation to blog on comparative physiology in the hopes that the discussion about this branch of science could grow broader and deeper via the blogosphere. For others thirsting…
Zuska of Thus Spake Zuska Says...
Perhaps you have noticed our newly redesigned front page, and on that page, a link to the Rightful Place Project. In his inaugural address, President Obama promised to restore science to its "rightful place". Seed Media Group is starting a dialog in response, asking the question "What is science's rightful place?", through Seed Magazine and ScienceBlogs. Our benevolent overlordz have asked us to offer our thoughts in response to this question. You'll see at the Rightful Place page that you can submit your own thoughts on this question, and there is a link to the Rightful Place blog to…
Dave
On Wednesday December 14, 2006, my stepfather and friend, Dave Williams, died very suddenly of a heart attack at the age of 61. Unlike many of the people who've been memorialized on ScienceBlogs, Dave was not a celebrity academic or a scientific luminary. His contributions to humanity will not be heralded in newspapers or immortalized in textbooks, but that makes them no less real and no less worthy of recognition. Dave was a wonderful man with a wonderful brain, and those who knew him will understand what I mean when I say that his passing has left a Dave-shaped hole in the universe. There…
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