Author Archives: curiouscat

The Subtly Different Squid Eye

The subtly different squid eye by PZ Myers:

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 was prompted by a recent publication on the structure of squid rhodopsin.

Superficially, squid eyes resemble ours. Both are simple camera eyes with a lens that projects an image onto a retina, but the major details of these eyes evolved independently – the last common ancestor probably had little more than a patch of light sensitive cells with an opsin-based photopigment. The general properties of this ancient eye can still be seen in modern eyes. They detect light with a simple molecule called retinal that is capable of absorbing a photon, changing its shape from the 11-cis form to the all trans form; basically, it flips from a chain with a kink to a straight chain. Retinal is imbedded in a protein called opsin. When retinal changes shape, it changes the shape of the opsin protein, too, which can then interact with other proteins in the cell membrane.

The next protein in the sequence is called a G protein. G proteins are ubiquitous intermediates for many cellular processes; when a receptor, like opsin, is activated, it activates a G protein, which then activates other proteins, starting a signaling cascade. In the podcast, I compare this to starting an avalanche. Opsin is an agent standing on a hill; when it receives a light signal, it nudges a small boulder (the G protein), which then tumbles down setting a whole series of rocks in motion. The G protein is an intermediate which takes a small change, the initial nudge, and amplifies it into the activation of many other proteins.

Marketing Drugs

Melody Petersen, author of Our Daily Meds: How the Pharmaceutical Companies Transformed Themselves into Slick Marketing Machines on Bill Moyer’s Journal:

I actually thought that they were a lot about science. That’s what they tell the public. They are all about science and discovering new drugs. But as I started to follow their daily activities and talk to executives, I learned that really it was marketing that drove them.

According to Petersen, the rewards have been large. America has become the top consumer of prescription drugs in the world, with nearly 65% of the population on physician-prescribed medication. In 2005, Americans spent $250 billion dollars on such drugs. This consumption made pharmaceuticals the most profitable business sector in America from 1995-2002.
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We’ve come to a time when decisions on how to treat a disease have as great a chance of being hatched in a corporate marketing department as by a group of independent doctors working to improve the public’s health.

Unfortunately patients are driven more by marketing than medicine. Much worse though, doctors seem to bend to these patients marketing driven desires. Plus the corrupting influence of money on research and marketing to doctors seems likely a significant reason for the poor performance and high cost of USA health care.

Challenging the Science Status Quo

Challenging Science

When scientists question facets of existing theories or propose new ones, they present the best evidence available and make the strongest arguments they can to their colleagues. Colleagues in turn challenge that evidence and reasoning. The rigor of this process is what makes science such a powerful tool.
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Lynn Margulis wrote a paper, “The Origin of Mitosing Eukaryotic Cells,” which argued that eukaryotic cells – those with a true nucleus – arose when cells with no nucleus symbiotically incorporated other such cells to make new cells that could perform more functions. The paper was rejected by many journals, and when eventually published by The Journal of Theoretical Biology it was highly criticized. Margulis spent decades defending her work, but scientists now accept her suggested mechanism through which organelles such as mitochondria and chloroplasts evolved. Her suggestions about other organelles have not stood up to experimental tests, and are not as widely accepted.
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In 1982, Stanley Prusiner published an article on his research into scrapie – a disease in sheep related to Creutzfeldt-Jakob disease – which argued that the infectious agent was not a virus but a protein, which Prusiner called a “prion”. Because no one had heard of a protein replicating without a nucleic acid like DNA or RNA, many virologists and scrapie researchers reacted to the article with incredulity. When the media picked up the story, “the personal attacks of the naysayers at times became very vicious,” according to Prusiner. However, his critics failed to find the nucleic acid they were sure existed, and less than two years later, Prusiner’s lab had isolated the protein. Subsequent research provided even more support for prions, and in 1997 Prusiner was awarded the Nobel Prize in Physiology or Medicine.

Wind Power Potential to Produce 20% of Electricity Supply by 2030

Wind energy has been growing tremendously. In 2000 there were 2,500 megawatts (MW) of installed wind capacity in the United States. By the end of 2007, the U.S. installed capacity exceeded 16,000. A recent Department of Energy report sees the potential to provide up to 20% of our nation’s electrical supply via wind power by 2030.

Cosmology Questions Answered

A great list of Cosmology Questions Answered, including: Why do we think that the expansion of the Universe is accelerating? What is quintessence? What is the Universe expanding into?

Everything that we measure is within the Universe, and we see no edge or boundary or center of expansion. Thus the Universe is not expanding into anything that we can see, and this is not a profitable thing to think about. Just as Dali’s Corpus Hypercubicus is just a 2-D picture of a 3-D object that represents the surface of a 4-D cube, remember that the balloon analogy is just a 2-D picture of a 3-D situation that is supposed to help you think about a curved 3-D space, but it does not mean that there is really a 4-D space that the Universe is expanding into.

Brian Cox Particle Physics Webcast

TED webcast of Brian Cox discussing his work at CERN’s Large Hadron Collider. He does a very good job of explaining some of the basic science in understandable terms.

Running Out of Fish

I have posted before about the overfishing problems: Fishless Future – SelFISHing – Chinook Salmon Vanish Without a Trace. Here is an emotional article on the problem – How the world’s oceans are running out of fish

Ninety years of industrial-scale exploitation of fish has, he and most scientists agree, led to ‘ecological meltdown’. Whole biological food chains have been destroyed.
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In 2002, the year an EU report revealed that the Senegalese fish biomass had declined 75 per cent in 15 years, Brussels bought rights for four years’ fishing of tuna and bottom-dwelling fish on the Senegal coasts, for just $4m a year. In 2006, access for 43 giant EU factory fishing vessels to Mauritania’s long coastline was bought for Â£24.3m a year. It’s estimated that these deals have put 400,000 west African fishermen out of work; some of them now take to the sea only as ferrymen for desperate would-be migrants to the Canary Islands and Europe.
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Protecting up to 40 per cent of the world’s oceans in permanent refuges would enable the recovery of fish stocks and help replenish surrounding fisheries. ‘The cost, according to a 2004 survey, would be between Â£7bn and Â£8.2bn a year, after set-up. But put that against the Â£17.6bn a year we currently spend on harmful subsidies that encourage overfishing.’
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The Newfoundland cod fishery, for 500 years the world’s greatest, was exhausted and closed in 1992, and there’s still no evidence of any return of the fish. Once stocks dip below a certain critical level, the scientists believe, they can never recover because the entire eco-system has changed.

Engineering Graduates Again in Great Shape

Once again engineering and computer science graduates are receiving the highest starting salaries. Previous posts: Lucrative college degrees (2006) – starting salaries for engineers (2005) – High Pay for Engineering Graduates 2007.

According to a survey, these are the top-paying majors for 2007-08 bachelor degree graduates:
$63,616 — Chemical engineering (up 6.5%)
$59,962 — Computer engineering
$59,873 — Computer science (up 14.7%)
$58,252 — Industrial/manufacturing engineering
$57,821 — Mechanical engineering (up 5.7%)
$57,999 — Aerospace/aeronautical/astronautical engineering

Source: Spring Survey, National Association of Colleges and Employers

Engineering Jobs Top U.S. Skills Shortage List

Engineering positions are the most difficult jobs to fill for U.S. employers, according to Manpower Inc.’s 2008 Talent Shortage Survey released April 24. Of 2,000 U.S. firms responding, 22% said they had difficulty filling positions, ranking engineers, machinists/machine operators and skilled manual trades as the top three toughest positions to fill, respectively

Grads’ job prospects weakening by degrees

In one year, the former hydraulic repairman will have a bachelor’s degree in mechanical engineering from Purdue University Calumet. And, as far as he can tell, he can write his own ticket.

“I’m finding jobs pulling at me left and right,” he said last week at a manufacturing industry job fair at the college. “The professors told us there’s such a demand, if you go to a job fair, you can walk out with a job.”

Vela, 35, happens to be in a field where demand remains strong, despite the uneven economy. Overall starting wages for mechanical engineering grads will be up 3.4 percent this year, with an average salary offer of $56,429, according to the National Association of Colleges and Employers. For many other college grads looking for a job at this time of year, the prospects are not as sweet.

Starting salaries: What the future holds (UK)
Continue reading →

Curious Platypus Genome is No Surprise

Platypus Genome Found Fittingly Strange by Rick Weiss

a team of scientists has determined the platypus’s entire genetic code. And right down to its DNA, it turns out, the animal continues to strain credulity, bearing genetic modules that are in turn mammalian, reptilian and avian.

There are genes for egg laying — evidence of its reptilian roots. Genes for making milk, which the platypus does in mammalian style despite not having nipples. Genes for making snake venom, which the animal stores in its legs. And there are five times as many sex-determining chromosomes as scientists know what to do with.

“It’s such a wacky organism,” said Richard Wilson, director of the Genome Sequencing Center at Washington University in St. Louis, who with colleague Wesley Warren led the two-year effort, described today in the journal Nature.

Yet in its wackiness, Wilson said, the platypus genome offers an unprecedented glimpse of how evolution made its first stabs at producing mammals. It tells the tale of how early mammals learned to nurse their young; how they matched poisonous snakes at their venomous game; and how they struggled to build a system of fertilization and gestation that would eventually, through relatives that took a different tack, give rise to the first humans.

“As we learn more about things like platypuses,” Wilson said, “we also learn more about ourselves and where we came from and how we work.”

Very cool stuff. Related: Platypus genome explains animal’s peculiar features; holds clues to evolution of mammals – Platypus genome mapping boon for human and livestock researchers – Platypus genetic code unravelled – Weird Creatures – Evolution is Fundamental to Science – Long-Eared Jerboa – Cat Joins Exclusive Genome Club – Your Inner Fish

Elephants Classify Human Ethnic Groups that Hunt Them by Odor

Wash Your Clothes: Elephants Can Smell You a Mile Away

…in Amboseli National Park in Kenya. Elephants in the region encounter different ethnic groups, including the Maasai, whose young men spear elephants, and the Kamba, agricultural villagers who pose no threat at all.

The researchers observed elephants exposed to the scent from identical cloth garments, some worn by Maasai men, others by Kamba men and some that were unworn. The Maasai scent produced the strongest reactions, with elephants moving farther and faster to distance themselves from the odor source, often not stopping until reaching tall grass. The elephants also took far longer to calm down than those exposed to scents from the Kamba and unworn cloths.