Author Archives: curiouscat

2,000 Species New to Science from One Island

photo of squat lobster

Photograph by Dr Tin-Yam Chan, University of Keelung

153 scientists from 20 countries fanned out across the remote South Pacific island of Espiritu Santo, examining mountains, forests, caves, reefs, and water for all living organisms. In five months, they collected 10,000 species. Some 2,000 of these may be new to science.

This squat lobster, found in waters 150 meters (492 feet) deep, is one of the new species. Eighty percent of the world’s species remain to be discovered, notes French scientist Philippe Bouchet, one of the expedition’s leaders.

A World of Crabs from One Tiny Island

About 600 of these were crab species. The two-horn box crab is able to crack and peel open snails’ shells using a sharp “tooth” on its right claw to cut open shells and long, slender “fingers” on the left claw to yank out its prey.

Do Breast Tumors go Away on Their Own?

Authors of a new study hope to begin a debate challenging the conventional wisdom about early detection of breast cancer. In an article in today’s Archives of Internal Medicine, they ask: Do breast tumors ever go away on their own?

Researchers of this controversial article note that one type of cancer found through screening — a rare childhood tumor, called neuroblastoma — sometimes disappears. In the new article, researchers try to learn if the same phenomenon occurs with invasive breast cancers found with mammograms

The Natural History of Invasive Breast Cancers Detected by Screening Mammography

Conclusions: Because the cumulative incidence among controls never reached that of the screened group, it appears that some breast cancers detected by repeated mammographic screening would not persist to be detectable by a single mammogram at the end of 6 years. This raises the possibility that the natural course of some screen-detected invasive breast cancers is to spontaneously regress.

As with so much medical research the results are not completely clear. Studies need to be followed by more studies, which often lead to more studies. As long as progress is being made this is a perfectly reasonable course of scientific inquiry. And even if progress is not being made this can be perfectly reasonable – finding answers can be hard.

Snowflakes

Wilson A. Bentley pioneered the photography of snowflakes.

When he was seventeen years old, his parents bought him a bellows camera that had a microscope inside that could magnify the tiny snowflake from 64 to 3,600 times its actual size.
Bentley spent long hours in the bitter New England cold mastering the art of snowflake photography. After many failures, he photographed his first snow crystal in 1885, using a small lens opening that let in just a little bit of light but leaving the lens open for up to a minute and a half. He devoted the rest of his life to exploring these fascinating forms and photographed more than 5,000 snow crystals until his death in 1931.

The photo above was taken by Bentley in 1902 (see more).

HHMI on Science 2.0: Information Revolution

The Howard Hughes Medical Institute does great things for science and for open science. They have an excellent article in their HHMI Bulletin – Science 2.0: You Say You Want a Revolution?

Cross-pollination among research disciplines is in fact at the core of many other popular science blogs. Michael Eisen, an HHMI investigator at the University of California, Berkeley, is an avid blog reader who particularly enjoys John Hawks’ site on paleoanthropology, genetics, and evolution. A recent post there discussed a new sequencing of Neanderthal mitochondrial DNA. “It’s like a conduit into another whole world,” says Eisen.
…
The current extreme of collaboration via Science 2.0 is OpenWetWare.org. Begun in 2003 by Austin Che, who was then a computer science and biology graduate student at MIT, this biological-engineering Website uses the wiki model to showcase protocols and lab books: everything is open and can be edited by any of its 4,000 members.
…
“Most publishers wish open access would go away,” says Brown. It won’t. Major research-funding organizations, including NIH, HHMI, and the Wellcome Trust, now require their grantees to post their findings on openaccess Websites such as PLoS or PubMed Central within 12 months of publication in traditional journals. Publishers are pushing back, however, and in September, the House Judiciary Committee began holding hearings on whether the federal government should be allowed to require grantees to submit accepted papers to a free archive.

How Large Quantities of Information Change Everything

Scale: How Large Quantities of Information Change Everything

There’s another important downside to scale. When we look at large quantities of information, what we’re really doing is searching for patterns. And being the kind of creatures that we are, and given the nature of the laws of probability, we are going to find patterns. Distinguishing between a real legitimate pattern, and something random that just happens to look like a pattern can be somewhere between difficult and impossible. Using things like Bayesian methods to screen out the false positives can help, but scale means that scientists need to learn new methods – both the new ways of doing things that they couldn’t do before, and the new ways of recognizing when they’ve screwed up.

There’s the nature of scale. Tasks that were once simple have become hard or even impossible, because they can’t be done at scale. Tasks that were once impossible have become easy because scale makes them possible. Scale changes everything.

I discussed related ideas on my Curious Cat Management Improvement blog recently: Does the Data Deluge Make the Scientific Method Obsolete?

Canadian Meteorite Fragments Found

University of Calgary graduate student Ellen Milley poses with a fragment of a meteorite

Pictures of Canadian Meteorite Fragments

Planetary scientist Dr. Alan Hildebrand from the University of Calgary and graduate student Ellen Milley brought reporters to a site where they have found numerous meteorite fragments from the bolide that streaked across the sky in Western Canada
…
The fireball that streaked across western Canadian skies was witnessed by thousands, and Hildebrand believes it was a 10-ton fragment from an asteroid. Videos from surveillance and police cameras [see below] showed the meteor exploding before it hit the ground

Photo: University of Calgary graduate student Ellen Milley poses with a fragment of a meteorite in a small pond. By Geoff Howe, The Canadian Press.

Related: U of C team finds meteor fragments – Meteorite, Older than the Sun, Found in Canada (this is a different meteorite – story from 2007) – In Tunguska, Siberia 99 Years Ago – Meteorite Lands in New Jersey Bathroom
Continue reading →

von Neumann Architecture and Bottleneck

We each use computers a great deal (like to write this blog and read this blog) but often have little understanding of how a computer actually works. This post gives some details on the inner workings of your computer.
What Your Computer Does While You Wait

People refer to the bottleneck between CPU and memory as the von Neumann bottleneck. Now, the front side bus bandwidth, ~10GB/s, actually looks decent. At that rate, you could read all of 8GB of system memory in less than one second or read 100 bytes in 10ns. Sadly this throughput is a theoretical maximum (unlike most others in the diagram) and cannot be achieved due to delays in the main RAM circuitry.
…
Sadly the southbridge hosts some truly sluggish performers, for even main memory is blazing fast compared to hard drives. Keeping with the office analogy, waiting for a hard drive seek is like leaving the building to roam the earth for one year and three months. This is why so many workloads are dominated by disk I/O and why database performance can drive off a cliff once the in-memory buffers are exhausted. It is also why plentiful RAM (for buffering) and fast hard drives are so important for overall system performance.

Simple Webcasts on Evolution and Genes

Webcast from 23andme on human evolution. Continued: What are genes?, What are SNPs? (Single Nucleotide Polymorphisms), Where do your genes come from? and What is phenotype?. These webcasts provide an easy to understand overview. Sergey Brin, Google co-founder and husband of 23andme co-founder Anne Wojcicki. People have 23 pairs of chromosomes.

What are SNPs?:

For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome.
…
SNPs do not cause disease, but they can help determine the likelihood that someone will develop a particular illness. One of the genes associated with Alzheimer’s disease, apolipoprotein E or ApoE, is a good example of how SNPs affect disease development. ApoE contains two SNPs that result in three possible alleles for this gene: E2, E3, and E4. Each allele differs by one DNA base, and the protein product of each gene differs by one amino acid.

Where are the Senior Female Scientists

Why Are Senior Female Scientists So Heavily Outnumbered by Men? by Anna Kushnir

There is some funny math in the world of academic science. Take my graduate school for example: My class was made up of eight people — seven women and one man, or 7 to 1. He was Snow White and we were the seven dwarves — each with a remarkably appropriate nickname. I was Grumpy, should you be curious to know.

Snow White and at least four of the dwarves have continued on to postdoctoral research jobs. That is a 4 to 3 ratio of women who went on to do a post-doc to those that chose alternate career paths.

Everything is adding up so far, right? Lots of women are around. Lots of science is being done. All is well. The next set of numbers is slightly puzzling, however. That is the ratio of female to male professors in our department, at a well-respected academic institution, is 48 to 7 men to women.
…
The proportion of female faculty in her department, 14 percent, is exactly equal to the overall average from the top fifty US chemistry departments.

From her blog: Lab Life: I thought I wanted to be “normal”

The majority of researchers, in my experience, think that stress level, pressure, and time commitments all drop by a factor of ten the moment you step outside of the chemical-smeared walls of a lab. I have come to realize that’s a misconception. It’s just not true. I think that whenever one wants a career instead of a job, time, stress, pressure, and worry are the price to pay.

If all I wanted was a job with a steady income, I am pretty sure I could get it. I would be well-rested and calm, but would I be happy? Would I be alright staying put where I am, with nothing pushing me to reach the next step or rise to the next level? I don’t think so.

I have heard the words ‘ambition’ and ‘drive’ described as derogatory, when applied to people. Unfortunately, I think those are apt words to describe me (in addition to ‘tired’ and ‘often occasionally cranky’). It was an important thing for me to understand about myself and come to terms with. It’s just who I am.

The Science of Gardening

Photo of a bee by Justin Hunter

The Science of Gardening

Linda Chalker-Scott, an associate professor at Washington State University, is the author of The Informed Gardener and producer of the column “Horticultural Myths.” In The Truth About Garden Remedies: What Works, What Doesn’t, and Why, Jeff Gillman, associate professor at the University of Minnesota, is just as rational and informative
…
Do go ahead and dig in soil improvements, Chalker-Scott advises, for vegetable gardens or annual flowerbeds, in which nutrients need replacing yearly. But there’s really no need to dig organic amendments—manure and peat moss, etc.—into landscapes that are permanent. Treat those plantings of trees and shrubs as if they were forest ecosystems, not agricultural fields—wood chips and decaying leaves on top, no tilling-in of fertilizer.
…
It must drive both authors nuts to hear people say, “I’m an organic gardener. I never use chemicals.” Everything on earth is composed of chemicals.

The last line calls to mind the recent Royal Society of Chemistry attempt to reclaim the word chemical from the advertising and marketing industries: Â£1,000,000 for 100% chemical free material. A good example for our scientific literacy posts.

Photo by Justin Hunter.