Science blog trek

I need to get out more. There's so much interesting stuff out there. Here are some finds from a recent trek around the science blogosphere:

Sex in an MRI Machine

This piece from Stuart Coleman at Daily Irreverence is to get your attention so you keep reading. Don't show it to your maiden aunt Bertha. It has sexually explicit stuff in it, like penises and vaginas. But perhaps not the way they're seen in porn flicks. The title explains it all. This is actual, bona fide research. Wish I could read the grant proposal for this... so I could plagiarize it.

Omega-3 oils & marijuana may stave off Alzheimer’s

Here's one that may be of more interest to Bertha, courtesy of the Neurophilosopher. And it isn't just about fish oil, either. "In recent months, various studies have provided evidence that apple juice, a Mediterranean diet, cabernet sauvignon and curry can either reduce the likelehood of developing Alzheminer’s or reverse the cognitive impairment which is symptomatic of the disease. To that list we can now add omega-3 oils. And marijuana."

Origins of Gene Structure

Dan Rhoads at Migrations tackles some difficult questions in evolutionary theory. Specifically, how can we explain the evolution of the intricate gene expression process in eukaryotic cells? Do we need to resort to models of "genetic drift" as opposed to "adaptive selection"?

Conditions for the Emergence of Life

This is another one from Dan. He likes to deal with difficult, fundamental issues in molecular evolution, and nothing is more fundamental than the question of how life got started. This article just sketches some of the questions about how life could arise from a self-organizing chemical system.

DarkSyde's Open Science Thread for 10/7/06

DarkSyde, who also blogs (sometimes) at Unscrewing the Inscrutable, is a regular contributor at Kos's place, on both politics and science. He posts a regular article on Fridays, and short link fests like this one from time to time. This particular fest has an item about quantum teleportation. Maybe I'll write more about that later. But what was really interesting was the following item from Sean Carroll.

The Cell Is Like Tron

For biologists, I should note that this Sean Carroll is Sean M. Carroll, the cosmologist, not Sean B. Carroll, the evo-devo biologist. Anyhow, the item here is actually mostly for biologists -- a spectacular computer animation of the internal structures of a cell. But it will impress, if not astonish, just about anyone. Do not fail to take a look at it. If you want to know what's going on, there's some explanation here, where you'll also find a high-res version. (A faster/smoother high res version is here.) This thing was originally mentioned at Pharyngula. As a free bonus, Sean also throws in a couple of links for physicists.

Miscellaneous links, 8/24/06

We start off with some sites which have great collections of information in their respective subject areas.

Comparative Mammalian Brain Collections

As it describes itself, "This web site provides browsers with images and information from one of the world's largest collection of well-preserved, sectioned and stained brains of mammals. Viewers can see and download photographs of brains of over 100 different species of mammals (including humans) representing over 20 Mammalian Orders." Building upon this extensive visual information, there are also overviews of topics like brain evolution, brain development, brain architecture, and brain function.

BCI-info

One staple of much science fiction writing is the idea of Brain-Computer Interfacing (BCI) -- connecting living brains with computers and other electronic or mechanical devices. There are obvious mundane applications, such as brain diagnostics and control of prosthetic devices like artificial retinas and artificial limbs. Then there are more speculative applications like brain augmentation by connection to specialized computers, interfaces to large databases, teaching machines, and perhaps even storage and retrieval of individual memories. Put some sort of communications capability in the loop and you have electronic telepathy. But this isn't just science fiction. BCI research is actively going on. That's what this site is about: "BCI-info is an open international platform for Brain-Computer Interface research intended to provide information for scientists, patients, students, the media, and people from the general public interested in BCI technology."

Introduction to Linguistics

Would you like a quick, easy introduction to linguistics so you could get a grasp of what's common to most human languages and understand some of the issues that people like Noam Chomsky and Steven Pinker write about? Try the course put together by Sophia A. Malamud at the University of Pennsylvania. See the class schedule to access the course lectures.

The Virtual Embryo

Embryology and developmental biology are two of the most active areas in the life sciences. You need to understand the basics in order to appreciate hot topics like stem cells and evolutionary developmental biology ("evo-devo"). This site provides a great resource for learning about them. Topics covered include gametogenesis, embryonic development, the genetic regulation of development, organization of multicellular embryos, and cell differentiation. There are plenty of links to relevant external resources as well as a tutorial on devlopmental biology.

And here are some shorter articles about interesting recent research.

DNA or RNA? Versatile Player Takes a Leading Role in Molecular Research

RNA is chemically very similar to DNA, except that its backbone is made of a slightly different sugar molecule, one of its four bases is different from the analogous base in DNA, and RNA molecules are usually single-stranded, in contrast to double-stranded DNA. RNA was first understood in the form known as messenger RNA, which transcribes the information in a gene in order to construct a protein. However, there is another type of RNA that is chemically the same but has a different function. This is sometimes known as regulatory or "silencing" RNA. It is produced in the same way as messenger RNA, as a transcription of a special type of DNA gene. But its function is to regulate the production of proteins from messenger RNA. Silencing RNA is usually only about 20 base units long, but it performs its regulatory function by attaching to a complementary segment of messenger RNA, thereby inhibiting the construction of a protein.

Monster Tumors Show Scientific Potential in War Against Cancer

A teratoma is a cancer-like growth, consisting of a mass of partially differentiated cells. Teratomas can be quite large, and sometimes include mature tissues such as teeth and hair. Some teratomas originate from egg cells which begin to develop as if they had been fertilized, but without the developmental programming to progress like a normal embryo. They can be useful in stem cell research because they may be a good source of such undifferentiated cells. Since they also contain a variety of differentiated cell types, they can be used in cancer research as a test bed for new drugs.

Diving deep for answers

Sea anemones are primitive animals of the phylum Cnidaria. Other cnidarians include corals (belonging to the same class as anemones) and jellyfish. They seem to be the most primitive animals that have distinct types of tissue, such as mouths and tentacles and stinging cells. Cnidarians originated at least 600 million years ago, even before the Cambrian explosion. The study of sea anemones should help understand the evolutionary process which allows more complex animals with multiple tissue types to develop.

And the Evolutionary Beat Goes On . . .

Evolution is often thought of as a process that goes on only over long periods of time, like hundreds of thousands of years. But smaller changes can occur much more quickly, as in the coloration of insects in order to better hide from predators. Some recent research has demonstrated simlar rapid changes in humans that have occurred in the last 10,000 years. Such changes include responses to variation in diet. Others have to do with skin color, disease resistance, fertility, and reproduction. In each case, scientists have identified corresponding changes in human DNA that can be dated to recent times.

Miscellaneous links, 2006-06-09

Once again, a link fest...

Probing the antiworld

A free access article from the October 2005 issue of Physics World. (There's at least one in each issue, and it's usually worth the read.) This article describes how antimatter (antihydrogen) is actuall made in the lab. The ultimate goal is to allow a test of the CPT theorem by measuring the spectrum of antihydrogen.

Universe reveals its dark side

Another article from Physics World, the May 2005 issue. It provides a quick overview of what dark matter might be, and more detail on various experimental approaches to detecting dark matter. (Additional evidence is discussed here.)

Relativity at the centenary

One more article from Physics World, January 2005. Most physicists do not seriously doubt either special relativity or general relativity -- at least, not in almost all circumstances. But since relativity does not comport well with the other foundation of modern physics, quantum mechanics, there's plenty of reason to search for minuscule effects where relativity is not quite correct. The hope is that understanding such effets -- if they exist -- may give clues to how relativity needs to change in order to fit better with quantum mechanics. For instance, tests for violations of "Lorentz invariance", a key feature of special relativity, could tell us something about possible theories of quantum gravity, such as string theory. In another direction, tests of the inverse square law of gravitational attraction at small distances (under 10 mm) could indicate the existence of more than 3 spatial dimensions.

Brain's Darwin Machine

April 11, 2006 article from the Los Angeles Times. It describes a fascinating recent research finding. Every human brain contains roughly 100 billion (10¹¹) neurons. Brains of 3-year-olds actually contain twice as many neurons, and half of them die by adulthood. But even in adulthood, thousands of new neurons form every day and play a role in building new memories. Amazingly, most neurons are genetically different from all others. The new discovery is that this difference seems to be due to the insertion of a short sequence of DNA, called a "long interspersed nuclear element", at random locations in the genome. The distinctness of most neurons may help account for the vast amount of information and experience that brains are capable of encoding.

Regrow Your Own

April 11, 2006 article from the New York Times. Regenerative medicine is about discovering how to induce human bodies to regrow damaged parts, just as some amphibians and fish can. Experimental stem cell therapies receive the most attention in this field, but there's an alternative: employing the same (or similar) genetic programs that the amphibians and fish use. This involves mature cells at the location of damage reverting to a more immature state, forming a cell mass called a "blastema", which in turn develops into the appropriate body part. Humans may have the necessary genes to do this, but for unknown reasons they are not switched on. There is reason to hope for a way around this, because in fact there is one organ that actually can regenerate after substantial damage: the liver.

Fighting Cancer Through the Study of Sarcomas

Here's an article from the September-October 2005 issus of American Scientist. A sarcoma is a cancerous tumor of bone, fat, or muscle tissue. Sarcomas are less common than cancers of the blood or internal organs, but exhibit the same abnormalities. It's often noted that cancer is really a large number of different diseases, each reflecting some different combination of genetic damage. Such genetic problems tend to be studied in more detail in sarcomas, leading to diverse kinds of experimental treatments. The article gives a number of examples, which illustrate a variety of the different abnormalities that lead to cancer.

BioCarta

This is the only link in this collection to a whole site rather than a single article. BioCarta is a commercial enterprise that supplies "uniquely sourced and characterized reagents and assays for biopharmaceutical and academic research." Their customers are generally engaged in the field of "proteomics", which is the study of how proteins interact with each other and thereby control all processes in and between living cells. But BioCarta's site is less about their business than it is a fascinating catalog of known "pathways", which are biological programs made up of sequences of protein interactions that drive a particular cellular function, such as "apoptosis" (cell death) or regulation of the "cell cycle". Each pathway is described with both text and high-quality graphics. For example: the p53 signalling pathway -- p53 is a protein that has a key role in regulating the cell cycle, in order to prevent cell division if the cell's DNA has been damaged. Mutations in the p53 gene so that its protein malfunctions are very common in many types of cancer.

Miscellaneous links, 2006-04-22

Here's where I put interesting stuff I don't have time to write about in detail. Mostly it will be noteworthy Web sites or great articles that stand on their own without further commentary.

The Brain from Top to Bottom

A superb, interactive tutorial on brain structure and function. Covers most important topics, like memory, emotions, and the senses. It offers separate discussions on three different levels: beginner, intermediate, and advanced. Discussions are also classified in terms of level of physical organization (social, psychological, neurological, cellular, and molecular). Each discussion has many internal cross references to others, as well as external links on each page.

Questions and Answers About Avian Flu

Very good set of questions and answers by Denise Grady and Gina Kolata, published March 27, 2006 in the New York Times.

Nanotechnology: CTF Essays, Part 1

This is a press release from the Center for Responsible Nanotechnology, announcing a series of new research papers in which industry experts predict profound impacts of nanotechnology on society. A couple of the authors (Ray Kurzweil and David Brin) will be known to a fairly wide audience. Papers which have already been published are available here, along with forums for online discussion of the topics. (Press release also available here.)

Center for Responsible Nanotechnology

From the site: "The Center for Responsible Nanotechnology is a non-profit research and advocacy organization concerned with the major societal and environmental implications of advanced nanotechnology." Useful content of the site includes issues, external links, nanotech FAQ, glossary, and a blog.

KurzweilAI.net

Kurzweil is, among other things, a futurist. (More about him here or here, if you need it.) Have a look at his Web site if you're interested in any of the following: AI, virtual reality, life extension, nanotechnology, or robotics. (It could take weeks to get through all of it.)

MIT OpenCourseWare

As the name suggests, this is course material, such as syllabi, reading material, and sometimes lecture notes, from actual MIT courses. From the site: "a free and open educational resource for faculty, students, and self-learners around the world." It won't guarantee you'll ace your final in Quantum Field Theory. Or make up for the classes you cut in Developmental Biology. But it may help you learn a little about either of those subjects, and many others, if you haven't had the chance to crack a book on one of them before.

The Hundred Greatest Theorems

As rated by Paul and Jack Abad in 1999. Math grad student Nathan Kahl put the list up on the Web, with links to information about the theroems (when available), as well as links to biographical information on the mathematician credited with proving each theorem. Kahl also has a list of useful math links.