By now, everyone must be familiar with the inside out organization of the cephalopod eye relative to ours: they have photoreceptors that face towards the light, while we have photoreceptors that are facing away from the light. There are other important differences, though, some of which came out in a recent Nature podcast with Adam Rutherford (which you can listen to here), which was prompted by a recent publication on the structure of squid rhodopsin.
Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is “weird” or “odd” or worse, they imply that the animal is a chimera — “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”. No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What’s interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.
We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: “Genome analysis of the platypus reveals unique signatures of evolution.” This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.
There’s a clumsy little two-step move creationists like to make: first, point to dissent in the scientific community over real and often interesting issues at the edge of knowledge, and second, swap in their dissent over basics, like common descent, and pretend that the scientists are actually sharing in their ignorance-based concern. John Timmer has a good summary of a few genuine scientific arguments, contrasted with the bogus arguments creationists pretend are important.
There are some good and interesting questions out there. The creationists, and I include the phonies at the Discovery Institute among them, never ask them.
One other point Timmer brings up at the end: should the real scientific controversies be part of the public high school curriculum? He thinks not, and I agree — I’d rather the high schools prepared students with a general understanding of the most basic principles, rather than rushing off to pursue details with which the students won’t yet be able to cope, anyway.
I must urge you to steal buy this book: Illustrated Guide to Home Chemistry Experiments: All Lab, No Lecture (amzn/b&n/abe/pwll). The description makes it sound perfect.
Laboratory work is the essence of chemistry, and measurement is the essence of laboratory work. A hands-on introduction to real chemistry requires real equipment and real chemicals, and real, quantitative experiments. No existing chemistry set provides anything more than a bare start on those essentials, so the obvious answer is to build your own chemistry set and use it to do real chemistry.
Everything you need is readily available, and surprisingly inexpensive. For not all that much more than the cost of a toy chemistry set, you can buy the equipment and chemicals you need to get started doing real chemistry.
…
DIY hobbyists and science enthusiasts can use this book to master all of the essential practical skills and fundamental knowledge needed to pursue chemistry as a lifelong hobby. Home school students and public school students whose schools offer only lecture-based chemistry courses can use this book to gain practical experience in real laboratory chemistry. A student who completes all of the laboratories in this book has done the equivalent of two full years of high school chemistry lab work or a first-year college general chemistry laboratory course.
Ooooh, I wish this book had been around 15 or 20 years ago, when I could have infected my kids with it. Maybe I’ll have to wait a few years (many years!) and expose a grandkid to it … which will have an added advantage that the parents will have to deal with the messes and smells.
Odd thing, though: I looked through the table of contents, and there’s not one single solitary thing about chemistry prayers. How can the experiments possibly work?
My last Seed column is online, which reminds me (as if I weren’t uncomfortably aware already) that I have to finish up the next one today, which actually isn’t the next one, which is already done and submitted, but the one after that. These long leading deadlines force one to live a few months in the future…
You know, if you subscribed to the print magazine, you’d be halfway to my future already instead of living in my distant past.
The title gets the principal objection of any creationist out of the way: yes, this population of Podarcis sicula is still made up of lizards, but they’re a different kind of lizard now. Evolution works.
Here’s the story: in 1971, scientists started an experiment. They took 5 male lizards and 5 female lizards of the species Podarcis sicula from a tiny Adriatic island called Pod Kopiste, 0.09km2, and they placed them on an even tinier island, Pod Mrcaru, 0.03km2, which was also inhabited by another lizard species, Podarcis melisellensis. Then a war broke out, the Croatian War of Independence, which went on and on and meant the little islands were completely neglected for 36 years, and nature took its course. When scientists finally returned to the island and looked around, they discovered that something very interesting had happened.
There in the foaming welter of email constantly flooding my in-box was an actual, real, good, sincere question from someone who didn’t understand how chromosome numbers could change over time — and he also asked with enough detail that I could actually see where his thinking was going awry. This is great! How could I not take time to answer?
So here’s the question:
How did life evolve from one (I suspect) chromosome to… 64 in horses, or whatever organism you want to pick. How is it possible for a sexually reproducing population of organisms to change chromosome numbers over time?
Firstly: there would have to be some benefit to the replication probability of the organisms which carry the chromosomes. I don’t see how this would work. How is having more chromosomes of any extra benefit to an organism’s replicative success? Yes, perhaps if those chromosomes were full of useful information… but the chances of that happening are non existent and fly in the face of ‘small adaptations over time’.
Secondly, the extra chromosomes need to come from somewhere. I’m not sure about this, but I believe chromosome number are not determined by genes, are they? There isn’t a set of genes which determines the number of chromosomes an organism has. So the number is fixed, determined by the sexually reproducing parents. Which leads me to believe that if the number does change, and by chance the organism is still alive and capable of sexual reproduction, that the number will start swinging back and forward, by 1 or 2, every generation, and never stabilising. The chances of this happening are also very very slim.
Revere is thinking about how to grow meat without the animal. It’s a cool idea that’s been floating around in science fiction for a while now, but, well, of course it has problems, and Revere notes a couple.
The two biggest, as far as I can see from a quick perusal of the burgeoning literature, are finding a suitable nutrient to grow the cells in; and then growing tissue that has the proper texture for being a meat substitute. Animal meat is not just muscle cells but a complicated structure also containing connective tissue, blood and blood vessels, nerves and fat. Just growing up masses of identical cells isn’t sufficient. You have to reproduce an architecture.
I see those two problems as aspects of one much bigger problem. Muscle doesn’t grow in isolation: it’s always in a solid environmental context. It’s made up of cells that respond to activity in a way that enhances performance for the organism, and incidentally promotes flavor and texture and bulk for the delectation of the carnivore. So what do you need to make edible muscle mass, beyond a sheet of myocytes in a culture dish (which, I suspect, would have the texture of slime and would not sell well in test markets)?
An architecture is right. You need connective tissue to form a framework and you need a rigid but motile structure to do work and exercise the growing muscle. Then, because you want a piece of muscle larger than a drop, you need a delivery system for nutrients: a circulatory system, with a pump. This muscle in a vat is going to need a skeleton and a heart.
When I teach physiology, one of the organs I emphasize is the liver. It’s amazing how important a liver is to just about everything: growth, digestion, physical performance, reproduction, the whole shebang. Our cultured muscle will need a liver equivalent to support it. Even if we get rid of the digestive system entirely and feed this muscle mass on delivered supplies of pure glucose, amino acids, and various cofactors and enzymes, the liver is a primary regulatory agent for those substances.
Then we need an immune system. A huge lump of cells growing in a bath of sugar and amino acids is bacterial heaven — it’s going to need major antibacterial/antiviral support.
The more I think about it, the more I think people are going at it backwards. We shouldn’t be thinking about building muscle from the cells up, to create a purified system to produce meat for the market, we should be going the other way, starting with self-sustaining meat producers and genetically paring away the less commercially viable bits, like the brain. Instead of test-tube meat, we should be working on more efficient organisms that generate muscle tissue with the properties we want.
Guess what? Farmers have already been doing this! Look at the domestic cow and chicken and turkey: they’re far more brainless than their wild relatives, and have been reduced to as much stupidity and helplessness as possible, without compromising their ability to survive semi-autonomously and harvest nutrients from naturally occurring food sources. I don’t see all that much difference in the consequences between building up a functional meat producer from cells in a dish, and stripping down a functional meat producer from a line of domesticated animals. Both starting points are aiming at the same final result; I suspect that the top down procedure is more likely to achieve success in my lifetime.
I’m busy preparing my lecture for genetics this morning, in which I’m going to be talking about some chromosomal disorders … and I noticed that this summary of Fragile-X syndrome that was on the old site hadn’t made it over here yet. A lot of the science stuff here actually gets used in my lectures, so they represent a kind of scattered online notes, so I figured I’d better put this one where I can find it.
I haven’t even finished grading the last of the developmental biology papers, and already my brain is swiveling towards the genetics literature, as I get in the right frame of mind to teach our core genetics course in the spring. And, lo, here is a new paper in PNAS that addresses details of a topic I bring up every time.
There are a surprising number of heritable diseases that share a couple of common traits: they are neurodegenerative, causing progressive loss of neural control, and they also exhibit a phenomenon called genetic anticipation—they tend to get worse, with earlier onset and more severe affects with each generation. Some of these diseases may be rather obscure, for instance
Haw-River Syndrome (AKA Dentatorubral-pallidoluysian atrophy),
Friedreich Ataxia,
Machado-Joseph Disease, or
X-linked Spinal and Bulbar Atrophy Disease (AKA Kennedy Disease), but others you’ve probably heard of, like
Myotonic dystrophy and
Huntington Disease. These are dreadful diseases that are variable in their pattern of appearance, and have terrible symptoms, like loss of motor control, chorea, seizures, dementia, and eventually, death.
Jay Hosler has a new book out, Optical Allusions(amzn/b&n/abe/pwll). If you’re familiar with his other books, Clan Apis(amzn/b&n/abe/pwll) and The Sandwalk Adventures(amzn/b&n/abe/pwll), you know what to expect: a comic book that takes its science seriously. Hosler has a fabulous knack for building serious content into a light and humorous medium, just the kind of approach we need to get wider distribution of science into the culture.
This one has a strange premise. Wrinkles the Wonder Brain is an animated, naked brain working for the Graeae Sisters, and he loses the one eye they share between them — so he has to go on a quest to recover it. I know, it sounds like a stretch, but it works in a weird sort of way, and once you start rolling with it, you’ll find it works. Using that scenario to frame a series of encounters, Wrinkles meets Charles Darwin and learns how evolution could produce something as complex as an eye; talks about the sub-optimal design of retinal circuitry with a cow superhero; discovers sexual dimorphism with a crew of stalk-eyed pirates; learns about development of the eye from cavefish and a cyclops; chats with Mr Sun about the physics of radiation; there are even zombie G proteins and were-opsins in a lesson about shape changing. This stuff is seriously weird, and kids ought to eat it up.
It isn’t all comic art, either. Each chapter is interleaved with a text section discussing the details — you can read the whole thing through, skipping the text (like I did…), and then go back and get more depth and directions for future reading in the science. This is a truly seditious strategy. Suck ’em in with the entertainment value, and then hand ’em enough substance that they might just start thinking like scientists.
It’s all good stuff, too. A colleague and I have been considering offering an interdisciplinary honors course in physics and biology with the theme of the eye, specifically for non-science majors, and this book has me thinking it might make for a good text. It’ll grab the English and art majors, and provide a gateway for some serious discussions that will satisfy us science geeks. I recommend it for you, too — if you have kids, you should grab all of Hosler’s books. Even if you don’t have kids, you’ll learn a lot.
Jay Hosler also explains the intent of the project, and you can read an excerpt.
