A $48,000 Macintosh computer

I want one, but I’ll have to wait for the price to drop just a little bit…and I’m confident that the price will plummet in the next few years. It’s really just a stock Mac, but it has something special on it: a copy of your very own genome sequence. The whole thing. Oooh.

Give it a few years, and the price of sequencing your genome will drop to a few thousand dollars, and then below a thousand…and then I’ll be going for it. Unfortunately, at those prices they probably won’t throw in a new computer with it.

Space science in Minnesota

The Minnesota Planetarium Society has ambitious plans to rebuild and expand a planetarium and space discovery center in Minneapolis, and they’re trying to spread the news and build more support. They are having an event to do this:

Summer Solstice Celebration
Monday, June 22
4:00pm – 8:00 pm
Minneapolis Central Library
300 Nicollet Mall

This event is co-sponsored by the Library Foundation of Hennepin County. Here is your chance to — travel past the Sun out into the universe through the Society’s ExploraDome sky theater, that has been wowing school kids throughout Minnesota — learn something new about astronomy and telescopes from the Minnesota Astronomical Society, and — expose your kids to the world of Astronomy through astronomically-related games. We also hope you’ll take this opportunity to see the future site of the Minnesota Planetarium and learn more about how we can make it a reality.

ExploraDome shows will be held on the half-hour. The dome holds 25 at a time, so reservations are recommended. To reserve your spot, please send your name, phone number and time (by the half-hour) to the sally@mplanetarium.org OR 651-999-7300. The 6:30pm show is a special presentation in Pohlad Hall featuring our planetarium colleagues live from around the world, and is open to all.

Let’s build this!

i-95d52771a399f2688eab918892860879-planetarium.jpeg

So…soap bubbles must be designed!

You’ve probably noticed that as a soap bubble thins, it acquires a rainbow of iridescent colors across its surface. Or perhaps you’ve noticed that a film of oil on a mud puddle shows beautiful colors. These are common physical properties of thin film interference.

The way it works is that light entering a material with a higher refractive index is both reflected and transmitted. Some of the light bounces back with a partial phase shift, and some of it passes through. In a thin film, it passes through but doesn’t travel far before it hits another boundary, for instance between the film and the water underneath it, and again, some of it is reflected and some transmitted. This second reflected beam of light, though, is out of phase with the first, by an amount that depends on the thickness of the film. What that means is that certain wavelengths will be shifted in such a way as to reinforce the first reflected beam, generating constructive interference that will make that wavelength brighter. Other wavelengths will be shifted the same amount, but they will be out of phase with light in the first reflected beam — there will be destructive interference, and that wavelength will be damped out.

The net result: the light reflecting off the film will be colored, and the color will depend on the thickness of the film. It’s a simple physical process. Cephalopods use it to generate their colors — just by shifting thin reflecting membranes by a tiny distance of a fraction of a wavelength of light, they shift which wavelengths constructively and destructively interfere with each other, and thus change their color. Now engineers are exploiting the same principle to build television screens: they use a thin film that can be expanded by fractions of a wavelength of light by applying a voltage to build reflective color screens. This will be very cool. If you’ve got a Kindle or one of the other e-book readers, you know they use a reflective screen with no backlight that depends on ambient lighting to be visible…and that right now you only get shades of gray. With this technology, we’ll be able to have color electronic paper. I’ll be looking forward to it.

Unfortunately, we’ll also enable incomprehending gomers. Case in point: Casey Luskin thinks that thin-film interference patterns implies design. Well, actually, it’s stupider than that — he actually thinks that because TVs are being designed to use thin-film interference, and because cephalopod skin uses thin-film interference to generate color, that implies that cephalopod skin is also designed. I kid you not.

So we may soon have affordable, energy-efficient, cuttlefish inspired flat screen TVs and computer monitors everywhere. But of course, there’s no design overtones to see here folks. None whatsoever.

Right. And because trebuchets were designed to use gravity to generate force, and because rocks on mountains will tumble down due to gravity, avalanches are therefore designed. We make fire by design to produce the release of energy by rapid oxidation of carbon compounds; cells also oxidize carbon-containing compounds to produce energy; therefore, cells must have been set on fire on purpose. This is what the IDiots are reduced to: if something designed and something evolved make use of the same properties of our common physical universe, that means the evolved object must be designed, too. It’s ridiculous, but it’s all they’ve got.

Life Ascending

I admit, I was initially put off by the mere title of Nick Lane’s new book, Life Ascending: The Ten Great Inventions of Evolution(amzn/b&n/abe/pwll). I’m one of those many biologists who is adamant about the absence of direction in evolutionary history, and ascending just sounds too much like life climbing the rungs of the ladder of life, so I picked it up in a somewhat prejudicial mood.

Have no fear, though, I was won over. Right at the beginning, he admits that it is a subjective list; his criteria for including the ten chosen evolutionary innovations are that it had to revolutionize the living world, that it was important to a significant subset of life today, that it was a product of biological (not cultural) evolution, and that it had to be iconic — it had to symbolic and arrestingly interesting to human beings. That’s fair enough; one could write a book on just the evolved properties of prokaryotes, but yeah, operons and chemical sensing and secretion and motility are of vast importance, but they’re only going to be iconic to a rather restricted set of readers. And since my own personal interests run more to metazoan innovations, I’m not going to complain about a book that gives my hobby horses a more substantial run.

Even better, though, what enlivens the book is the biochemist’s perspective: Lane isn’t so much interested in the superficial matters of morphology, but in the emergence of new properties in the molecular machinery of the cell, and how it affects the world around us. Somehow, it always thrills me when we drill down right to the interactions of molecules to explain how biology works.

So here are the ten evolutionary inventions Lane describes.

  1. Origins of life: Where and how did life arise? A review of some of the models for abiogenesis.

  2. DNA: What conditions would allow for the synthesis of nucleotides? Where did the genetic code come from?

  3. Photosynthesis: The photosynthetic pathway is a combination of two very different functional pathways — what does this tell us about their evolution?

  4. Complex cells: How did cells become more complex? A chapter on horizontal transfer and endosymbiosis — borrowing and stealing and kidnaping by ancient cells.

  5. Sex: Why do we have sexual reproduction? A question that focuses on the cytological and genetic machinery.

  6. Movement: How do organisms get around? Cytoskeletons and motor proteins, and where they came from.

  7. Sight: How did vision evolve? A fairly wide-ranging discussion of opsins and crystallins and Hox genes and the weird glow of black smokers.

  8. Hot blood: Another chapter with a little taste of everything: respiration, metabolism, insulation, and how a key feature of our physiology affects everything.

  9. Consciousness: Where did our awareness come from? You won’t be surprised to learn that Lane is a materialist — the answer lies in the wiring of the brain.

  10. Death: Why do all organisms die, and why do we even have genes that contribute to senescence and death?

So the topics aren’t that biased: only three exclusive to multicellular animals, and six that are about eukaryotes almost exclusively — and even in those our prokaryotic heritage is discussed. And really, when you’re talking about genes and biochemistry, you can’t get away from the fact that you are dealing with genuinely universal processes.

The book is also a fun read, deep enough to give you some substance, yet clearly written with the general public in mind. If you aren’t a biologist or biochemist, don’t shy away — you will be able to read this book, and you will learn a lot from it. When I was reading it, I was thinking this would be a really enjoyable text to build a freshman seminar course around. The chapters are readable and each one addresses an interesting topic in biology, bringing up both current research and pending questions, and it’s meaty enough to spark some good discussions.

Save the submersibles!

Go sign this petition to maintain the tools for sea exploration at Florida Atlantic University. They’re trying to get a thousand signatures…we can do that in no time at all.

The Johnson-Sea-Link I & II submersibles are owned and operated by Harbor Branch Oceanographic Institute (HBOI) at Florida Atlantic University (FAU) in Fort Pierce, Florida. They are launched from the HBOI research vessel R/V Seward Johnson, a 204-ft ,purpose built ,state of the art platform redesigned in 1994 which displaces 1282 tons and has a 6,000 nautical mile range. An experienced captain and crew constantly maintain the R/V Seward Johnson as part of the University-National Oceanographic Laboratory System (UNOLS) Fleet of research vessels. A team of highly skilled sub pilots operate, maintain and upgrade the submersibles according to strict safety protocols. The Johnson-Sea-Link submersibles were built in 1971. Almost four decades, 9,000 dives and continuous upgrades and improvements later, the Johnson-Sea-Link I submersibles and II, along with their support ship the R/V Seward Johnson, remain invaluable platforms for exploring the oceans.

&hellip:

Unfortunately, the current administration of HBOI has announced its decision to sell the R/V Seward Johnson and retire the JSL submersibles in spite of a lack of technologies with similar or better capabilities at HBOI, FAU or any other institution on the East coast of the U.S. While some argue that this expensive technology is outdated and tied to its mother ship, this view is not shared by the scientific community. The Alvin submersible operated by Woods Hole Oceanographic Institute in Massachusetts is 10 years older, and still performs between 150 and 200 dives a year. No one considers the Alvin 40-year old technology, or criticizes its dependence on the research vessel Atlantis for its deployment. It is still considered a valuable workhorse. While NOAA has just awarded HBOI a 22.5 million dollars grant to be a Cooperative Institute, in part due to their ability to perform oceanographic study with such tools as the R/V Seward Johnson and JSL submersibles, it is unclear whether these assets will be supported by that grant money. Unless a new source of funding is found to support these technologies, the current administration will continue their plans to abandon these technologies. Maintaining and operating these technologies is expensive, and the HBOI administration lacks the funds to continue to support these assets. Thus, it is critical for the State of Florida to invest in these amazing technologies to further our ocean exploration and our scientific progress.

Since FAU is a state university, the submersibles and research vessel are property of the State of Florida and the taxpayers should have a say in choosing whether these amazing technologies which are helping us discover and protect our underwater assets should be maintained. These are expensive technologies to maintain, but their benefits far outweigh their costs. If you believe that the state of Florida should invest in science, education and technology, please sign this petition to indicate to our legislators that you believe the HBOI ship and submersibles should be saved from sale or retirement and supported by the state of Florida.

Darwinius masillae

This is an important new fossil, a 47 million year old primate nicknamed Ida. She’s a female juvenile who was probably caught in a toxic gas cloud from a volcanic lake, and her body settled into the soft sediments of the lake, where she was buried undisturbed.

i-7c1a746bdef84283eca6d89008d65a2c-darwinius.jpeg

What’s so cool about it?

Age. It’s 47 million years old. That’s interestingly old…it puts us deep into the primate family tree.

Preservation. This is an awesome fossil: it’s almost perfectly complete, with all the bones in place, preserved in its death posture. There is a halo of darkly stained material around it; this is a remnant of the flesh and fur that rotted in place, and allows us to see a rough outline of the body and make estimates of muscle size. Furthermore, the guts and stomach contents are preserved. Ida’s last meal was fruit and leaves, in case you wanted to know.

Life stage. Ida is a young juvenile, estimate to be right on the transition from requiring parental care to independent living. That means she has a mix of baby teeth and adult teeth — she’s a two-fer, giving us information about both.

Phylogeny. A cladistic analysis of the fossil revealed another interesting point. There are two broad groups of primates: the strepsirrhines, which includes the lemurs and lorises, and the haplorhines, which includes monkeys and apes…and us, of course. Ida’s anatomy places her in the haplorhines with us, but at the same time she’s primitive. This is an animal caught shortly after a major branch point in primate evolutionary history.

She’s beautiful and interesting and important, but I do have to take exception to the surprisingly frantic news coverage I’m seeing. She’s being called the “missing link in human evolution”, which is annoying. The whole “missing link” category is a bit of journalistic trumpery: almost every fossil could be called a link, and it feeds the simplistic notion that there could be a single definitive bridge between ancient and modern species. There isn’t: there is the slow shift of whole populations which can branch and diverge. It’s also inappropriate to tag this discovery to human evolution. She’s 47 million years old; she’s also a missing link in chimp evolution, or rhesus monkey evolution. She’s got wider significance than just her relationship to our narrow line.

People have been using remarkable hyperbole when discussing Darwinius. She’s going to affect paleontology “like an asteroid falling down to earth”; she’s the “Mona Lisa” of fossils; she answers all of Darwin’s questions about transitional fossils; she’s “something that the world has never seen before”; “a revolutionary scientific find that will change everything”. Well, OK. I was impressed enough that I immediately made Ida my desktop wallpaper, so I’m not trying to diminish the importance of the find. But let’s not forget that there are lots of transitional forms found all the time. She’s unique as a representative of a new species, but she isn’t at all unique as a representative of the complex history of life on earth.

When Laelaps says, “I have the feeling that this fossil, while spectacular, is being oversold,” I think he’s being spectacularly understated. Wilkins also knocks down the whole “missing link” label. The hype is bad news, not because Ida is unimportant, but because it detracts from the larger body of the fossil record — I doubt that the media will be able to muster as much excitement from whatever new fossil gets published in Nature or Science next week, no matter how significant it may be.

Go ahead and be excited by this find, I know I am. Just remember to be excited tomorrow and the day after and the day after that, because this is perfectly normal science, and it will go on.

Laelaps has some serious reservations about the analysis — the authors may not have done as solid a cladistic analysis as they should, and its position in the family tree may not be as clear as it has been made out to be.

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, Smith BH (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. doi:10.1371/journal.pone.0005723.

How to build a dinosaur

I’ve been reading a new book by Jack Horner and James Gorman, How to Build a Dinosaur: Extinction Doesn’t Have to Be Forever(amzn/b&n/abe/pwll), and I was pleasantly surprised. It’s a book that gives a taste of the joys of geology and paleontology, talks at some length about a recent scientific controversy, acknowledges the importance of evo-devo, and will easily tap into the vast mad scientist market.

It is a little scattered, in that it seems to be the loosely assembled concatenation of a couple of books, but that’s part of the appeal; read the chapters like you would a collection of short stories, and you’ll get into the groove.

The first part is about Horner’s life in Montana, the Hell Creek formation, and dinosaur collecting. Hand this to any kid and get him hooked on paleontology for life; I recall reading every book I could get my hands on that talked about Roy Chapman Andrews as a young’un, and it permanently twisted me…in a good way. This will have the same effect, and many people will think about heading out to Garfield County for a little dusty adventure. I know I am — all that stands in my way is South Dakota.

A good chunk of the book is about molecules and how they show the relatedness of dinosaurs to birds, and to the work of Horner’s former student, Mary Schweitzer, who discovered soft tissue in T. rex bones. Horner presents a good overview of the subject, but is also appropriately cautious. You’ll get a good feel for the difficulty of finding this material, and for interpreting it; he clearly believes that these are scraps of real T. rex tissue, but how intact it is, what kinds of changes have occurred in it, and how much information will be extractable from these rare bits of preserved collagen (or whatever) is left an open question.

Finally, the subject of the title…Horner was an advisor to the Jurassic Park movies, and right away he dismisses the idea of extracting 65 million year old DNA in enough quantity to reconstitute a dinosaur as clearly nothing but a fantasy. That’s simply not how it can be done. But he does have a grand, long-term plan for recreating a dinosaur.

What is it? Why, it’s developmental biology, of course. Development is the answer to everything.

Here’s his vision, and I found it believable and captivating: start with a modern dinosaur, a chicken, figure out the developmental pathways that make it different from an ancient dinosaur, and tweak them back to the ancestral condition. For instance, birds have lost the long bony tail of their ancestors, reducing it to a little stump called a pygostyle. In the embryo, they start to make a long tail, but then developmental switches put a kink in it and reduce it to a stub. If we could only figure out what specific molecules are signaling the tissue to take this modern reducing path and switch them off, then maybe we could produce a generation of chickens with the long noble tails of a velociraptor.

My first thought was skepticism — it can’t be that easy. There may be a simple network of genes that regulate this one early decision to form a pygostyle from a tail, but there have been tens of millions of years of adaptation by other genes to the modern condition; we’re dealing with a large network of interlinked genes here, and unraveling one step in development doesn’t mean that subsequent steps are still competent to respond in the ancient pattern. But then, thinking about it a little more, one of the properties of the genome is its plasticity and ability to respond in a coherent, integrated way to changes in one part of a gene network. That capacity might mean you could reconstitute a tail.

And then, once you’ve got a tailed chicken, you could work on adding teeth to the jaws. And foreclaws. And while you’re at it, find the little genomic slider that controls body size, and turn it up to 11. What he’s proposing is a step-by-step analysis of chicken-vs.-dinosaur decisions in the developmental pathways, and inserting intentional atavisms into them. This is all incredibly ambitious, and it might not work…but the only way to find out is try. I like that in a scientist. Turning a chicken into a T. rex is a true Mad Scientist project, and one that I must applaud.

One reservation I have about this section of the book is that too much time is spent dwelling over ethical concerns. Need I mention that real Mad Scientists do not fret over the footling trivia of the Institutional Review Board? These are chicken embryos, animals that your average member of the taxpaying public finds so inconsequential that they will pay to have them homogenized into spongy-textured slabs of yellow protein to be slapped onto their McMuffin. Please, people, get some perspective.

As for respecting the chickens themselves, what can be grander and more respectful than this project? I would whisper to my chickens, “With these experiments, I will take your children’s children’s children, and give them great ripping claws like scythes, and razor-sharp serrate fangs like daggers, and I will turn them into multi-story towers of muscle and bone that will be able to trample KFC restaurants as if they were matchboxes.” And their eyes would light up with a feral gleam of primeval ambition, and they would offer me their ovaries willingly. I’d be doing the chickens a favor. Maybe some chicken farmers would have cause to be fearful, but I wouldn’t be working on their embryos, so let them tremble.

Oh, all right. Horner is taking the responsible path and putting some serious thought into the ethics of this kind of experiment, which is the right thing to do. It’s also the kind of project that will generate serious and useful information about developmental networks, even if it fails in its ultimate aim.

But I have a dream, too. Of a day when biotechnology is ubiquitous, and middle-class kids everywhere will have a cheap DNA sequencer and synthesizer in their garages, and a freezer with handy vectors and enzymes for directed insertional mutagenesis. And one day, Mom will come home with a box of fresh guaranteed organic free range chicken eggs, and Junior’s eyes will glitter with a germ of a cunning plan, fed by a little book he found in the library…and 30-foot-tall fanged chickens will triumphantly stride the cul-de-sacs of suburbia, and the roar of the dinosaur will be heard once again.

Embryonic similarities in the structure of vertebrate brains

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

I’ve been doing it wrong. I was looking over creationist responses to my arguments that Haeckel’s embryos are being misused by the ID cretins, and I realized something: they don’t give a damn about Haeckel. They don’t know a thing about the history of embryology. They are utterly ignorant of modern developmental biology. Let me reduce it down for you, showing you the logic of science and creationism in the order they developed.

Here’s how the scientific and creationist thought about the embryological evidence evolves:

i-0fbb95c437feb7bb89110acb6f8e6326-brcorner.gifScientific thinking

An observation: vertebrate embryos show striking resemblances to one another.

An explanation: the similarities are a consequence of shared ancestry.

Ongoing confirmation: Examine more embryos and look more deeply at the molecules involved.

i-c1503e12cd6cf804a7bbd33bdcee007f-tiny_gumby_trans.gif

Creationist thinking

A premise: all life was created by a designer.

An implication: vertebrate embryos do not share a common ancestor.

A conclusion: therefore, vertebrate embryos do not show striking resemblances to one another.



[Read more…]

Obama’s speech to the National Academies of Science

The president spoke to the NAS today, and he made some great promises: increases in funding for science and science education, an investment in training new teachers in science and math, a political commitment to get better advising in science untainted by ideology. He specifically promised 3% of the GDP to go to research in science and technology.

Listen to it in an NAS podcast, or read the transcript. It’s a good speech, except for the very last line, which was incredibly stupid…but I’ll overlook it as a mindless platitude.