Category Archives: science

Weekend Update 5/9/2020: The Best of Cephalopods, the Worst of Cephalopods

This isn’t my typical Weekend Update. We’re all suffering from anxiety fatigue, outrage fatigue, bad news fatigue, and so on. So I’m not sharing any of the news stories that caught my eye after posting yesterday’s Friday Five. I’m going to post something cool and sweet and science-y that a friend brought to me attention:

This thread about a woman who is a squid scientist who put up signs in her window and set up sidewalk chalk so neighbors can ask science questions about squids and the like, and she would write answers!

Click on the tweet and read the whole thread. It’s adorable!

Danna Staff, the scientist in question, also has a blog. This is her post from which I stole the title of this update: The Best of Cephalopods, The Worst of Cephalopod.

She’s also got a book coming out this fall that you can pre-order now: Monarchs of the Sea: The Extraordinary 500-Million-Year History of Cephalopods.

A giant bee-killing hornet!

Click to embiggen infographic

This is not science fiction or a horror movie!

So, there’s an invasive hornet species that’s been spotted in my state which we would really like to get rid of: WSU scientists enlist citizens in hunt for giant, bee-killing hornet.

There’s a photo on that page of a person holding one of the dead hornets and my god, it looks scary!

And it is scary, this thing’s sting can be fatal to humans who have no allergy to bees.

The hornets love to attack honey bee hives, eat not just the adult bees, but all the larva and pupae, as well. So it’s more bad news for agriculture if this species gets established.

There’s an app you can put on your phone to report sightings of invasive species. It’s also got lots of fascinating information about the invasives and how they disrupt ecosystem. Check it out!

Coffee, coffee, everywhere — and why half of what you know about it is wrong

“There is no such thing as strong coffee, only weak people...”
“There is no such thing as strong coffee, only weak people…”

I have been drinking coffee since I was 12 or 13 years old—in other words, for 45 years! During that time the amount and types of coffee I drink has varied. Growing up in a working class family in the central Rockies, meant that for many years the kind of coffee I drank would be sneered at by a lot of coffee afictionadoes. Cheap, canned ground coffee for the percolator, instant coffee for when you don’t have the time to make a full pot. My father and both grandfathers had the kinds of jobs where they took a lunch box and a big thermos full of coffee with them each day they went to work.

So for more than 45 years I’ve been around coffee and coffee lovers, as well as consuming a lot of coffee myself. And I have spent a good portion of those 45 years having to debunk commonly held beliefs about coffee’s affect on one’s body. I thought I had heard everything, but a couple of years ago when the topic of coffee came up in an online discussion, someone made a joke about coffee making you poop. Or, I should say, I thought they were making a joke. But I encountered it a few times again over the next few months, and then it seemed that everyone on the planet knew as an absolute certainty that coffee is a natural laxative of such power that if forces you to run to the bathroom a few minutes after finishing the cup.

This puzzled me in part because 1) I had never experienced this effect, and 2) while some of the men who drank a lot of coffee around me when I was a kid would occasionally make crude comments about how many times they had to take a piss because of the coffee (and that they didn’t want a third cup because they didn’t want to take another piss soon), no one had ever mentioned needing to take a dump. And I guarantee you that a couple of my uncles would have had some very colorful jokes based on it if they had ever observed a correlation between drinking coffee and needing to poop.

So, I did some research, and while it is easy to find a lot of web pages that promote the idea, if you restrict your reading to pages that cite medical studies, you find out that, yeah, it’s a myth. There was one study in the 1990 that seemed to show an increase in the muscle movements of the colon a few minutes after drinking coffee—but only in about 28% of the subjects. And, most medical people who commented on the study were quick to point out that the study didn’t demonstrate that this increase in activity was enough to create a laxative effect. Another study a few years later couldn’t reproduce the results with coffee alone—they only measured the increase if the person drank the coffee (either regular or decaf) along with a meal of at least 1000 calories. That would seem to indicate that maybe it isn’t the coffee that’s the issue, it’s filling up the stomach and kicking the digestive system into full gear that causes the movement further down.

Lots of people insist that drinking coffee makes them need to go. Among the many critiques raised by other researchers concerning these studies and the anecdotal evidence is people are overlooking the possibilities of both a pavlovian effect and habits. If you generally drink coffee shortly after waking up most days (because you set up the automatic coffee maker on a timer each night, for instance), and you usually eat dinner at roughly the same time each night, your body may just be ready to go by morning. The coffee is a coincidence.

As the article I linked to above also mentions, the oft repeated notion that drinking coffee, tea, and other beverages containing caffeine actually dehydrates you is also a myth. Coffee, it turns out, is not a diuretic.

I want to pause here and point out that I’ve heard the admonition against drinking coffee because it supposedly dehydrates you from nurses and other medical personnel ten times more often I hear it from anyone else. This is the reason that anytime someone starts telling me that one should eat or do this, or refrain from eating or doing that because their doctor told them that I have to fight not to roll my eyes before urging them to do some of their own research.

My favorite is that people still cite studies from the 1950s that showed a correlation between coffee drinking and heart disease (among other things). Because those original studies made two errors that created a false correlation: they didn’t control for tobacco use, and they didn’t separate data by the gender of the subject.

Turns out that back when smoking was much more prevalent than it is today, there was a high correlation between coffee use and smoking. In other words, people who drank a lot of coffee were more likely to also be heavy smokers. Once you think about the neurological properties of caffeine and nicotine, that makes sense, both substances are mood regulators. Anyway, turns out that most of the statistic correlation vanished once you accounted for the smoking.

A tiny bit of statistical correlation remained, but if you then separated the data and compared only coffee drinking men to non-coffee drinking men, and similarly only comparing coffee drinking women to non-coffee drinking women, the correlation completely vanished. Why? Well, coffee drinking men on average drink between 10-20 percent more coffee today than the average woman. Given that on average men outweigh women by a bit more than 10 percent, and the amount of caffeine one must consume to produce a given result varies by body mass, it makes sense that coffee drinking men will consume at least 10% more coffee than women. Completely separate from any lifestyle questions, it is a biological fact that merely being male increases one’s chances of developing heart disease or high blood pressure.

This is a great reminder that correlation doesn’t necessarily mean causation.

There have been many more recent studies that have shown there is no link between coffee consumption and coronary artery disease or stroke. That is, no link between regular coffee and those diseases. Oddly enough, people who drink a lot of decaf seem to have a slightly increased risk of certain types of coronary disease, though at this time no one knows why.

Anything that people indulge in—if it isn’t perceived as a necessity for survival—comes under a lot of scrutiny from others. There are always people who thinking you shouldn’t indulge in the activity at all, or that you shouldn’t do it more than they do, and so on. So that’s one reason coffee accumulates these misperceptions and why people repeat them indefinitely. More generally, people place a lot more weight on their own perceptions and anecdotal evidence of people who agree with them than they do to logic, statistics, and reproducability.

The science indicates that coffee doesn’t have most of the negative effects most people associate with it. So you can enjoy it guilt free. And if you’re one of those people who don’t enjoy or use it or all, that’s absolutely fine. Just stop ragging on other people for doing it. None of us are giving you grief for your oxygen habit, are we?

“Coffee: a warm, delicious alternative to hating everybody every morning forever.”
“Coffee: a warm, delicious alternative to hating everybody every morning forever.”

Flying by (Click to embiggen) (Click to embiggen)
We’ve come a long way from the morning in June, 1965, when I watched my first NASA launch, live. I’m pretty sure that Walter Cronkite was the narrator of my adventure. And by long way I do mean literally. The furthest from the Earth’s surface that Gemini 4 got was about 155 nautical miles. New Horizons has traveled about 3,000,000,000 miles (that 3 billion, yes, billion-with-a-B) to do its Pluto flyby.

The Gemini launch was the first one that was broadcast live, around the world, by satellite. So a lot of people watched the launch. And it was a great flight. Ed White (Edward H. White II) become the first person to space walk, exiting the capsule in a spacesuit with a camera. NASA only let him stay out 20 minutes (actually, they were telling the other astronaut, James A. McDivitt, to get White back in sooner, but White was trying to stay out as long as he could). White and McDivitt could communicate to each other over an intercom line that was part of the tether, but it didn’t connect with the exterior radar to the ground. On top of that, the primary communication system with the ground was having some problems (the VOX unit at McDivitt’s end didn’t correctly identify when McDivitt was talking, so it kept cutting in and out and odd times, so he had to switch to the push-to-talk mechanism).

NASA didn’t want White outside of the capsule during any of the periods when the capsule was out of range of a tracking station (we didn’t have quite as extensive a network of tracking stations around the world back then, so there were a few points in the orbit where we were out of communication with the capsule).

I’ve been a space geek at least since 1965. Probably longer, but the Gemini 4 launch is the earliest one I remember watching (and apparently drove everyone crazy talking about it for weeks after).

So, yes, I’m pretty excited about our flyby of the planet Pluto (if you’re one of those deluded people who adhere to the totally ridiculous redefinition, don’t bother arguing; a scientific definition of an class of object should depend upon the objectively measurable properties of that object only, not the presence or absence of other objects in its vicinity). I can’t wait until we start receiving the images New Horizons is taking today. We’re going to learn so much!

New Horizons races past Pluto in historic flyby

Everything you need to know about Tuesday’s Pluto encounter

NASA’s First Encounters with Planets in the Solar System

Dumb arguments against legal protections for transgender people, part 4

I’ve written before about dumb arguments people make for why there shouldn’t be legal protections for transgender people. And here’s one I haven’t tackled:

The Bible says it’s a sin!

You might want to read the whole book before you make that claim:

There is neither Jew nor Greek, there is neither slave nor free, there is no male and female, for you are all one in Christ Jesus.
—Galatians 3:28

The usual Biblical arguments about transgenderism ignore this verse, or try to claim that it’s being metaphorical about how god judges people. And then they point to verses in the Bible about how god created each person, or the verses about women covering their hair and so on to infer a definitive statement from god. But they’re wrong, as I’ll explain below… Continue reading Dumb arguments against legal protections for transgender people, part 4

Not this stuff, again!
We’re having a teeny bit of snow. Compared to the winter a lot of other people have had, we’ve been getting off easy. But that doesn’t mean I won’t grouse about it.

I’ve been checking up on the blog by Professor Cliff Mass (he teaches meteorology at the U of Washington, and was once a grad student of Carl Sagan). I’ve been following his weekly weather bit on a couple of the local NPR stations for years, where he nerds out about the science of weather. Today’s “nowcast” about our current series of alternating cold and warm fronts.

He was talking about the various computer models that they run, and how as they run them again and again they all change in the same way. He said, “Meteorologists call this dprog/dt or dmodel/dt (those who know some calculus will understand the name!).”

To unpack that joke, in math we are often concerned with rates of change. So we’ll talk about dx/dy, with the “d” referred to delta or change, and the “x” and “y” each being variables representing some quantity you might be monitoring, so “dx/dy” can be transliterated into English as “the change in x in relationship to the change in y.” Which sounds weird and abstract until I point out that every time you look at the speedometer on your car, it’s showing the “the change in distance in relationship to the change in time.” Most of the time we in physics and other physical sciences, the variable “t” represents time, so “dt” is “the change in time.” So Cliff’s comment about “dprog/dt” would be “the change in [the result from the] program in relation to the change in time” and “dmodel/dt” would be “the change in [the result from the computer] model in relation to the change in time.”

Anyway, it made me think of what may be my new favorite rate of change: dsnow/dt, “the change in the amount of snow in relationship to the change in time.”

And let me just say, I hope the slope of that curve goes negative sooner, rather than later. (Which is a nerdy way of saying I want the dang snow to go away!)

Fact isn’t meaning

Some years ago, while working on a collaborative science fiction project, one of the other people mentioned that they had read that chimpanzee DNA is more than 98% identical to human DNA. “It only takes that little 1% to make a huge difference!”

I had seen articles quote this figure as well, but since the human genome project was still underway at the time, I was a little skeptical that it was accurate. However, one of my friends showed me a reference to a paper in a peer-reviewed journal where the statistic came from, and a little research seemed to indicate that it was true. So I accepted it, occasionally quoted it myself, and didn’t think about it.

Until I read a book about the human genome project, which talked about that old statistical claim in particular, and explained exactly how it came about.

If complicated science theories or statistics make your head spin, don’t panic! I’m going to explain it in a way that will not cause you any distress.

Imagine that you have printed out the text of a pair of books that are roughly the same length. You have printed it out single-sided, double-spaced, and in comfortably-sized font. Now, you take a pair of scissors to the first book, and you start cutting each page up—you don’t cut them up randomly, you cut them so that you have several thousand little pieces of papers, each one of which has one and only one word on it.

Now, you sort them. You make a pile of all of the slips of paper that have the word “the” on it. You make another pile of all the slips that have the word “blue” on it, and so on, until you have a bunch of piles of the little slips of paper, each pile containing however many instances of a single word.

Pick the ten biggest piles, only, and discard the rest. Now count the number of slips of paper in each of your ten piles, and write down the number of times each word occurs in the book you cut up.

Now, go repeat the whole process on a second book, and when you’re done, compare the two lists. Calculate by what percentage each varies on each word, and then average that variation out.

When you’re done, you find that there is a 98% match between a Harry Potter book and Fifty Shades of Grey. “Look!” you declare, “They’re practically the same book!”

But you haven’t compared the two books, you’ve only counted words and compared counts of the most common words between the two books. If you perform this treatment on any books written in the same language, you’re going to find a match.

And I think everyone realizes, when I explain it this way, that what you’ve done does not measure how similar the books are.

Of course this makes you wonder what the scientists were thinking when they did something very similar to the DNA of humans and chimpanzees.

To be fair, the scientists who authored the original paper never claimed that humans and chimpanzees only varied from each other by 1 or 2 percent. They said that they found a similarity in the number and distribution of certain combinations of base pairs of the portions of the chromosomes compared of about 98%. They knew that they weren’t comparing the entire genome, because no one had mapped the entire thing for either species.

At the time, the methods we had for analyzing DNA were crude. We could separate chromosomes, we could pull out certain sequences and count those, but there was a lot we couldn’t do.

We also assumed that the long, repetitive bits at the end of each chromosome were junk, or filler, but new research is beginning to cast doubt on that.

Make no mistake, the more we study both species’ chromosomes, we keep finding a very high amount of similarity between us. Chimps and Bonobos both are clearly very closely related to us. But we aren’t “practically the same species.”

My point is, that 98% was a fact. It was even a true fact, but it was a very specific fact: when comparing certain portions out of the whole DNA. of each species, and when counting building blocks, without much regard to how those building blocks relate to each other, the number of those building blocks is about 98% the same in each species.

Before we can know what that fact means, we need to know a whole lot more facts and a much better understanding of the context.

Cousins, part 1

In The Human Blueprint: The Race to Unlock the Secrets of Our Genetic Script, science writer Robert Shapiro at one point explains that if you pick any two people at random on the street, it’s nearly impossible to go back more than six hundred years before finding a common ancestor. Yes, even if the two people appear to be of completely different races.

There are several caveats, the biggest being that is isn’t impossible, it’s just that the probability has gone down to such an incredibly small number (there were a bunch of zeros between the decimal point and the 1 in the percentage he gave), that for most purposes it might as well be impossible. There are pockets of human population that have been isolated for many more generations than covered in 600 years, of course. But they’re very small.

He also explained how for most of human history most people lived their entire lives within 30 miles of the place they were born, which was usually the same community where both their parents lived, and their parents before them, and so on. So most everyone in a particular community were related to each other, at least distantly.

That doesn’t contradict the previous statement, beacuse all you needed was a small fraction of people to occasionally wander far afield before finding someone to have a family with, and in a matter of a dozen or so more generations, most of the population of said insular community have inherited at least some genes from that one wanderer, and are now all distantly related to everyone back in his old community. They just don’t know it.

Humans have been doing this for hundreds of thousands of years, long before modern technology made world travel and relocation commonplace.

In other words, we’re all cousins, of one sort or another.