Penumbral Lore; the Shadows of Science

It’s going to take me a little while to get back into the rhythm of writing in this blog, so forgive me if I start out a bit slowly. I was going to begin with a story about prehistoric fashion, but a search for primary sources showed that the archaeologist only published in Russian.

I found an interesting story about TB in Homo erectus, but it’s either too recent to have hit the web or is available with a subscription only. Just be aware that the inference that the infected Homo erectus had dark skin is questionable.

Then there’s the whole hobbit issue. Ever since they were discovered there has been debate back and forth about whether the Homo floresiensis were a race of humans or a separate species has been lobbed back and forth. A recent article in Science, “Mutations in the Pericentrin (PCNT) Gene Cause Primordial Dwarfism“, with over two dozen authors, suggests that the hobbits were humans suffering from a particular form of dwarfism. Here is some criticism by blogger Greg Laden, be sure to check out the comments.

In other news - some of you may have noticed that some of my web badges have gone. I’ve moved them to my new craft blog Eye of the Beholder. In the I’ll be adding ‘yarn work’ posts over there, so if that’s your interest update your blog rolls…

Today the first flurries of snow actually stick to the ground, and give that ‘powdered sugar’ effect which will be so boring in a few weeks, but is still nice at the moment. Today I indulged myself in my annual ritual of going barefoot in the snow, just once, just to prove I still can. Today I told the girls to make sure their snow boots still fit, because if we wait until the first big snow storm the stores will all be sold out (ridiculous, but no stores around here ever re-order snow boots, no matter how the winter turns out).

Today is not too early or too late for this kind of snow, pretty typical, actually, but it reminded me that I hadn’t posted anything about climate change yet.

This is a particularly good time for it, because at this very moment, in Bali, the UN is holding a major Climate Change Conference. Not surprisingly, there has been concern about the carbon emmissions generated in getting scientists from all over the world to travel to Bali. Also not suprisingly, there is apparently a virtual conference going on in Second Life, so those who would rather not (or can’t afford to) go physically can participate as well.

The conference started two days ago, and already the first major alarming story has come out of it. Apparently the tropics are expanding much faster than models have predicted they would. A free subscription is required to read the article online, but here’s the abstract:

Nature Geoscience
Published online: 2 December 2007 | doi:10.1038/ngeo.2007.38

“Widening of the tropical belt in a changing climate”

Dian J. Seidel1, Qiang Fu, William J. Randel & Thomas J. Reichler

Some of the earliest unequivocal signs of climate change have been the warming of the air and ocean, thawing of land and melting of ice in the Arctic. But recent studies are showing that the tropics are also changing. Several lines of evidence show that over the past few decades the tropical belt has expanded. This expansion has potentially important implications for subtropical societies and may lead to profound changes in the global climate system. Most importantly, poleward movement of large-scale atmospheric circulation systems, such as jet streams and storm tracks, could result in shifts in precipitation patterns affecting natural ecosystems, agriculture, and water resources. The implications of the expansion for stratospheric circulation and the distribution of ozone in the atmosphere are as yet poorly understood. The observed recent rate of expansion is greater than climate model projections of expansion over the twenty-first century, which suggests that there is still much to be learned about this aspect of global climate change.

Timed to coincide with the beginning of the conference, activists from the Rising Tide Movement put up a false press release, claiming that the USCAP (US Climate Action Partnership) a consortium of a number of major businesses, had committed to a 90% reduction in greenhouse gas emission by 2050. I’m not so sure what they hoped to achieve by this. The USCAP caught it very quickly and set out their own press release to clarify the situtation.

Another hoax of interest, last month a pseudonymous writer perpetrated an elaborate hoax on climage change deniers, by creating a faux publication and seeing who would take the bait.

Not a hoax, but probably a good candidate for the Ig-Nobel, a paper soon to be published “Who pays for the ‘beer fridge’? Evidence from Canada“ by Denise Young of the Department of Economics, University of Alberta, assigns a disproportionate amount of Canada’s greenhouse emissions to beer drinkers who often keep the old inefficient refrigerator around after buying a new one.

In other words, let’s Blame Canada.

This morning I dreamed that Clarissa DeNetherlanden (sp?) and Greg Taylor had split up.

I’ve never met Greg or Clarissa, but I follow Decoder Ring Theatre, their biweekly radio drama. In the dream, I realized that they were gone because suddenly Trixie Dixon (girl detective), or was it Kit Baxter…? had a new partner, her faithful masseur, who helped her fight crime and worshipped her every breath. There were a few brief lines about the old partner and then the story went off.

I woke up and was concerned about them for a few minutes. After all, the first year with a new baby is a difficult one, and things do happen. It took me a couple of minutes to separate the dream knowledge (the change in show format) from real life knowledge (they’re married, and they have a baby named Max, who’s adorable).

As it happens, I know another couple who produce a podcast drama. Steve Wilson produces Prometheus Radio Theatre, and his lovely wife Renee often appears on that. I spoke to Steve earlier this week, and my DH and he auditioned for some community theater together. They don’t show any signs of marital problems. Could that have something to do with the dream? But why wouldn’t I just have dreamt about them directly?

My own DH has a podcast, the Secret Frequency. I co-hosted the second episode, and will be on the third (which should air tomorrow). That one isn’t a drama at all, though, it’s more of a ‘news and views’ piece, and it’s definitely DH’s baby. If we were ever to split, he would definitely have custody of the podcast.

So I’m thinking about dreams this morning, where they come from, and all the things attributed to them. Not just the folklore symbolism of dreams, but what function they have biologically. My current understanding was that dreams are believed to help ‘process information’ in learning in some way, but I thought it would be fun to track down how, and how much is actually known.

Not much, apparently. Google scholar brought me an article from Annals of Neurology, vol 56 Issue 4 pp 583 - 586, “Total dream loss: A distinct neuropsychologiceal dysfunction after bilateral PCA stroke”, by Matthias Bischof, MD and Claudio L. Bassetti, MD. This article describes a 73 year old patient who lost her ability to dream, but not the REM phase of sleep. I also found an article in NEUROLOGY 2005;65:1010-1015, “Aggressive dream content without daytime aggressiveness in REM sleep behavior disorder“ by M. L. Fantini, MD, MSc, A. Corona, MPs, S. Clerici, PhD and L. Ferini-Strambi, MD, which established that patients who move around a lot while dreaming (presumably lacking normal sleep paralysis) have agressive, violent, non sexual dreams but don’t seem to be more agressive than normal volunteers in daily life.

A specific search for dreams and learning brought me a citation from Science 2 November 2001: Vol. 294. no. 5544, pp. 1052 - 1057, “Sleep, Learning, and Dreams: Off-line Memory Reprocessing“ by R. Stickgold, J. A. Hobson, R. Fosse, and M. Fosse, which claims to permit “…an objective and scientific study of this dream formation and a renewed search for the possible functions of dreaming and the biological processes subserving it.” An article in Neuron Volume 44, Issue 1, 30 September 2004, Pages 135-148, “Memory Consolidation in Sleep Dream or Reality“ by Robert P. Vertes seems to report that sleep itself has no function in learning, to say nothing of dreaming.

A specific search for ‘dream function’ found an article describing various cycles which influence dreaming - Sleep Medicine Reviews, Volume 8, Issue 5, Pages 403-424 (October 2004) “Chronobiological features of dream production“ by Tore A. Nielsen. Tore A. Nielsen, along withDon Kuiken, Geneviève Alain, Philippe Stenstrom and Russell A. Powell, also published “Immediate and delayed incorporations of events into dreams: further replication and implications for dream function“ in the Journal of Sleep Research Volume 13 Issue 4 Page 327-336, December 2004, which detailed how long events take to work themselves into our dreams.

A search on keywords ‘dream necessary’ revealed “Memory Loss Is Not Equal to Loss of Dream Experience: A Clinicoanatomical Study of Dreaming in Patients with Posterior Brain Lesions“, published in the Journal Neuro-Psychoanalysis: An Interdisciplinary Journal for Psychoanalysis and the Neurosciences Volume 8, Number 2 / 2006, Pages 191-198 by Calvin Kai-Ching Yu, where memory loss did not seem to be related to dream loss. I also found a paper in the Journal of Cognitive Psychotherapy, Volume 16, Number 1, 2002 , pp. 39-53(15) by Arthur Freeman and Beverly White, “Dreams and the Dream Image: Using Dreams in Cognitive Therapy“. Clearly, they’re not the first therapists to suggest that dreams have clinical use, they’re just the authors of the article I found discussing it (and the article discusses the use of dreams in a specific type of therapy).

So I was coming to the conclusion that far less is known about the function and importance of dreams, but still I was sure that someone had established that dreams (and not just sleep) are necessary for mental hygeine if not mental health. Finally, I googled ‘dream deprivation’, and I came across “Physiology and Psychology of Dreams“ by Alan S. Eiser in Seminars in Neurology 2005; 25: 97-105, which seems to be an overview article of the state of the field, which basically says there are lots of theories about the importance and function of dreams and the subject is controversial.

Still, like most people, I am fascinated by dreams (at least by my own dreams), and I think that they are in some manner and fashion important.   Now that NaBloPoMo is almost over I might start journalling my dreams again.  Maybe I’ll even start a second blog to post them in, because I think I’ve subjected you all to enough ‘dream talk’ for a while.

I’m recovering nicely from yesterday, but I still feel as though my head were stuffed with cotton batting.   I’m going to  stick to to a very short post today, one of the quantum weirdness experiments I referred to earlier.  Also, watch the skies tonight, there should be a very good view of Mars near the moon.

In “Quantum Zeno effect” by Wayne M. Itano, D. J. Heinzen, J. J. Bollinger, and D. J. Wineland Time and Frequency Division, National Institute of Standards Technology, Boulder, Colorado 80303, the invesitgators provide a demonstration of the Uncertainty Principle.   In this experiment, the Beryllium ions ⁹Be⁺, which have been ‘trapped’ and ‘laser cooled’ can exist in one of two energy states (see my “periodic post” for a refresher in quantum states). An RF pulse then transmitted energy back into the cooled ions, adding enough energy to ‘push’ all of the ions into the higher energy state. 

The thing is, measuring the energy levels of the ions had a definite effect on their energy levels.  If they were measured frequently enough during the process, none of the ions would absorb enough energy to ‘kick them up’ to the higher level.   Note that, for the purposes of this experiment, the ‘observer’ which was needed to restrickt the energy state refers to the laser beam, not to any sentient observer.   (Still, plenty freaky enough)

I recall the first time I ever had a migraine. It was not just painful, it was downright bizarre. I could not shake the impression that my head had been replaced by a giant tick, perched somewhat unsteadily on my shoulders and holding on by means of tiny, sharp legs. For me, migraines are triggered by stress, or by insufficient or disrupted sleep, or by sinus congestion. When I have a migraine, it typically manifests as a terrible, throbbing pain centered around my left temple, a sensitivity to light and sound, extreme tiredness, and a sense that my body (particularly my head) is shifting and changing in some terrible way - occasionally so severe that the only way I can convince myself my face is not dissolving is to touch it. I have tried the prescription migraine medicine Imiprimine, but it didn’t work for me. Or rather, it worked poorly. The pain was less, the hallucinations were worse. I ended up doing what I usually do when I have a migraine - sleeping for the better part of three days.

Migraines run in my family. My father used to get “ocular” or “opthamalgic” migraines - he would lose his vision and (also) sleep for hours. Many people get vision disruption before the onset of headache symptoms, these are called ‘auras’. My neurologist informed me that any awareness of an oncoming migraine, any recognizable warning symptoms, were considered to be a form of aura.

I recognized my own aura starting around 10 this morning. Nothing as clear as vision loss, but a vague sense of being tired, an unusual awareness of my head, and the feeling of something ‘looming’ over me. I took 440 mg of Naproxen Sodium as soon as I recognized the symptoms, and the sense of impending doom drew back, somewhat, although I’m still not at my best.  If I end up with a full fledged migraine tomorrow I’ll try to drag myself out of bed long enough to type you an even more incoherent description of what it feels like.  

According to “Thickening in the somatosensory cortex of patients with migraine“, by Alexandre F.M. DaSilva, DDS, DMSc, Cristina Granziera, MD, PhD, Josh Snyder and Nouchine Hadjikhani, MD, and published in NEUROLOGY 2007;69:1990-1995, there are recognizable changes in the structure of the brain associated with migraine.  It is unclear, at this point, whether they are caused by, or the result of, the condition.

cFor your reading and viewing pleasure, you are invited to compare the abstract of “Pericardial pathology 900 years ago. A study and translations from an Arabic medical textbook.” by Rabie E. Abdel-Halim, FRCS Ed and Salah R. Elfaqih, FRCS to the “pubcast”:

which is a creative commons release.

I really enjoy the cross disciplinary thinking here.   It’s a 900 year old study of the heart, and it’s discussed in terms of how the research was done and what kind of collaboration went into producing the book.  

It’s also a nice introdution to SciVee TV.   SciVee (still in alpha) hosts science videos for all levels of user, from elementary school to science professional.   It will be interesting to see where they go with this, and I intend to keep an eye on it for future post material.

Well, ‘new’ is always an awkward thing to say about a dinosaur. Nigersaurus taqueti (pictured to the right) lived about one hundred ten million (110,000,000 or 1.1 x 10⁸ years ago.

According to Project Exploration (the picture at right comes from their ‘press package’) the skeleton was discovered in 1997, and was named after Nigeria (the country he was found in) and Dr. Taquet, who looked for dinosaur fossils in the 1960’s, but didn’t find them.

Although I could find a publication dating back to 1999 on this, “Sahara and the Uneven Rate of Skeletal Evolution Among Dinosaurs” (PDF download) I hadn’t heard anything about it at all until about a week ago. It’s been in the news a lot lately because the odd, super-straight jaw inspired some paleontologist to call it a ‘Flintstones Lawnmower’.

I can’t help but be distracted by the way the CGI reminds me of a video game. Not a criticism, since good CGI is good CGI, and I’m sure that the video game industry will really love Nigersaurus, but I still find it disconcerting.

It would be particularly problematic to designate the genus Xenoposeidon as ‘new’. The dinosaur itself probably lived about a hundred thirty million (1.1 x 10 years ago, and a vertebra was excavated by one Phillip James Rufford in the 1890’s, somewhere near Hastings. The Museum of Natural History acquired it in 1893.

Mike Taylor found the vertebra in the Natural History Museum in January of 2006. It had been e. Details are available in Mike Taylor’s blog. More details have just been published in Paleontology v. 50 part 6, in “An Unusual New Neosauropod Dinosaur From the Lower Cretaceous Hastings Beds Group of East Sussex, England” (PDF download)

It’s known only by athat single vertebra (pictured to the left, in a santa hat. Can’t even tell a dinosaur to wait until after Thanksgiving (j.k. - the picture was from Mike Taylor’s Christmas cards - last year). To be honest, my sister-in-law started playing carols this past weekend, and she’s behind the local mall by about a week. It’s enough to drive you batty. Remember when the day after Thanksgiving was when the decorations started going up? It defined the season. Now you’re getting Christmas advertising in July, and decorations before Halloween… grumph, grunt, growl.

Never mind. Dinos - cool, even if they are dressed up in out of season holiday clothes!

Zombies

Last week, my youngest got a text message from her cousin-in-NYC that he was going to Haiti to deal with “A Voodoo Curse”. This week, she got another one from him, about going to Haiti because of “…the Zombie Curse”. I couldn’t convince her it was the same thing.

I can, however, point you to archaeological evidence for zombies*. I can also point out that Max Brooks is not the only zombie researcher (zombologist?) to refer to. An especially dedicated one has taken this video of Zombies in central park.

… I would be remiss were I not to share this with you -
It’s got a creative commons attribution-noncommercial license, so if you just ripped it from me that would be OK, but I hope you’ll get it from Jonathon Coulton instead.  It’s my newest ringtone!

The Scientific Method

…and here you thought I’d find a way to link the two! I just wanted to make sure that I had a definition of what the scientific method actually is somewhere in the blog, and not just a working definition of science as a whole. So here it is, right below the Zombies!

First of all, there are lots of different ‘methods’ involved in science, it’s an organic process (as in it grows naturally from one step to the next). For a good discussion, see the Wikipedia Article or find a Science Fair Guide online.

The basic, bare boned description follows.

1. Collect data and observations (CAREFULLY)
2. Come up with an idea which works with the data you have (well label this phase hypothesis)
3. Make predictions from your hypothesis (if this really is true, then that will happen when I…)
4. Perform experiments to test those predictions, this generates more data
5. Really check that the results fit the hypothesis

EVERY point in the method should be documented, every experiment should be verifiable, and others should have enough information about what you did to repeat the experiment. Sometimes other hypothesis might also predict the same experimental results, in which case it should (hopefully) be possible to develop experiments where the results differentiate between the two… Basically, there’s a whole ‘peer review’ process, which means that other scientists get to pick apart your hypothesis, experimental design, data and conclusions before they hypothesis is generally accepted. At that point it becomes a theory.

Rinse, repeat.

String Theory, for example, is often denigrated as being ‘non scientific’ because it doesn’t make verifiable predictions. So maybe it’s better described as being a hypothesis than a theory. Except that it did the string model did ‘predict’ gravity, which is pretty impressive. Except that we all knew about gravity before then, didn’t we? Yes and no. I’ll be getting to String Theory eventually (I hope), but not until I’ve worked through more quatum mechanics here. In any case, the LHC (Large Hadron Collider) (which should go online in May of next year) will make all kinds of experiments possible. As I understand it, there is at least one string theory variant which makes predictions suitable for testing in it.

Scientific Laws are not the same as theories, but that’s the subject of a whole separate post.

Steve Irwin Day

This really should have had a post of it’s own, yesterday, but I didn’t know it was coming. Fans should check it out. I’ll mark my calendar for next year…

I couldn’t stop laughing after reading about what Franklin’s making for Christmas, so I thought I’d do a yarn post today.

Glow in the dark yarn has been available for a while now. Nightlights is one brand which is fairly conventional. It’s nylon. You expose it to light and it glows for several hours. The University of Manchester has apparently developed an electric yarn, Note, in particular that “Weaving or knitting the yarn in a particular manner, so that more yarn per unit area is achieved, improves the luminance of the EL yarn.”

This is pretty cool, from the point of view of a knitter, but thinking like a geek, I looked around for more ‘hi tech’ yarn. What I found out is that nano-fibers can be ‘electrospun’ to create yarns. More details about the properties of nano-yarn were presented last week at a Nanoelectric Materials Conference in Salt Lake City, but I’m having a hard time figuring out what that would mean in terms of industry, or for the knitter. How long would it take to knit a pair of socks with nano-yarn, anyway?

The UTD Nanotech Institute makes an intriguing mention of “a yarn that has been woven into a multifunctional electronic textile” made from carbon nanotube fibers. TMS Online ‘highlights’ a whole bunch of high-tech textiles, including nano clean fibers and yarns which turn on your lights.

OK, I’m sure there are a great many serious and sober uses for these materials, but at the moment it’s the fun factor which is attracting me here.

Tagging this ‘better living through chemistry’

A good place to start in discussions of the possibility of communicating with life from another planet is with Drake’s Equation:

N=R* x f_p x n_e x f_l x f_i x f_c x L

It says that N (the number of extra terrestrial species which might be able to send us recognizable signals) equals the average rate of star formation in our galaxy, times the fraction of those stars which have planets, x the average number of suitable planets per system, x the fraction of them which eventually develop life, x the fraction of those where life develops intelligence, x the fraction of those which develop a technological civilization (one which generates signals we could pick up) x the length of time they release those signals.

For the purposes of this argument, we’re looking at life which is very similar to terrestrial life, with chemistry based on Carbon, Oxygen and Hydrogen. At some future time we might take a look at Silicon/Sulfur chemistry, once a staple of SF novels but pretty out there, because hydrogen bonding won’t happen with Sulfur the way it does with Oxygen… So, basically, suitable planets have to have some quantity of liquid water in order for life to develop.

When Frank Drake came up with his equation, back in 1961, it was purely a theoretical exercise - how many planets might there be, and how many of them might have recognizable intelligence. Things have changed (a little) since then, in that we can now actually identify planets. As of this writing, there are 264 extra solar planets cataloged online. A couple of them from this past year are particularly exciting.

 

The most recent of these (as in, reported within the past week) is the fifth planet to be discovered orbiting the star 55 Cancri. 55 Cancri is a star very much like the sun, and the fifth planet is in the orbital zone which makes liquid water a real possibility. True, the planet is a lot more like Saturn than the Earth, but maybe it has moons. 55 Cancri is 41 light years away, so their inhabitants (if any) could point radio recievers at Sol and pick up “Strangers in the Night” by Frank Sinatra, or “These Boots are Made For Walking” by his daughter, Nancy, or, if they can decode television signals they could be treated to the first season of Batman.

 

The most Earthlike planet ever discovered was reported this past April. This one orbits a red dwarf (not to be confused with “Red Dwarf“) known as Gliese 581, very closely. It’s ‘year’ is about two weeks long. Gliese 581 is so cool, however, that this puts it within the ‘life zone’ and it could have liquid water. It’s about five times as massive as the Earth, and may be as small as 1.5 Earth diameters. This one is about 20 light years from earth, so listeners there might get “La Bamba” or maybe watch “Remington Steele” after Pierce Brosnan got jerked around as not bond, or catch the first season “Star Trek, TNG”.

That is, assuming that the signals would have enough strength to be decoded after 20-40 years of travel, but that’s the assumption we make when we scan the skys for alien signals, so it’s what I’m going with here.

Actually, this is very cool and exciting, and deserves some first class geeking out over. I’m just feeling a bit worn out today - my husband’s podcast will probably need another home if anyone’s going to be able to subcribe to it, and I’ve been playing around with it all day… Oh, well.   I took a moment to watch this video, taken on halloween night by the japanese space station Selene while orbiting the moon (as described in The Great Beyond). Amazingly cool stuff. Remember ‘the face on Mars’? Well, I’ve got this wonderful screen capture of a yin-yang mandala from the moon!