June 2007 – David Bradley

Free offline science magazines

Well, it’s the weekend again and the last thing anyone should be doing is sitting in front of their computer, but, hey, you don’t always have a choice, right? You have to keep up with all that reading, just to stay ahead of your game. Well, there is an alternative, and it’s right here under your nose on Sciencebase. It’s called extra silico visualated textual assimilation, or “reading” to you and me.

It often involves the selection of an analog textual disseminator from one’s own shelving or that of the local library or bibliographic outlet. It can, however, also involve the retrieval of a papyric derivative accumulated missive product, such as a newspaper or magazine, which may reach your domicile via the postal service.

What am I talking about? You may well wonder! Free science magazines, that’s what. Check out the Sciencebase science mags section for qualified free subscriptions to a wide range of bio, pharma, chemical, engineering, and biotech publications, including BioTechniques and Drug Discovery Today to which I am a past contributor, Bio-IT World, and Small Times. Every valid subscription helps support my weekday words on Sciencebase, costs you absolutely nothing, and gets you something free to read for those truly offline moments in your life. We all need them.

Ragworm Ragtime

Ragworm When I was a youngster I used to do a spot of sea fishing on the freezing cold north east coast. It wasn’t so much a hobby as an obsession at one point. Key to success was a plentiful supply of lugworm which could be dug from the wet golden sand at lowtide and stored ready for the next angling venture, while ragworm, which have a nasty bite, came from the local fishing bait supplier. Never would it have occurred to my 11-year old self that these lowly creatures could harbour the secrets of our own evolution.

However, apparently it does. Detlev Arendt of the European Molecular Biology Laboratory has been studying the multifunctional neurones that sense the environment and release hormones in vertebrates (including ourselves), flies, and worms. The last common ancestor of all of these creatures must provide the evolutionary basis of our modern brains that endow us with the skills to varying degrees of success to dig up ragworm, take part in fishing trips, and ponder our origins.

Hormones control growth, metabolism, reproduction and other biological processes. In humans, as indeed in all vertebrates, the chemical signals are produced by the hypothalamus and other specialist brain centres and secreted into the blood for circulation around the body. This signalling system is not, it turns out, the preserve of those creatures with a backbone. Arendt and his colleagues now believe that the hypothalamus and its hormones have their evolutionary origins in an ancient worm-like creature that lived hundreds of millions of years ago and is the common ancestor of vertebrates, flies, and worms.

Hormones work slowly, on the whole, and have body-wide effects. Insects and nematode worms use hormones, but the specific molecules they use are very different from their vertebrate counterparts.

“This suggested that hormone-secreting brain centres arose after the evolution of vertebrates and invertebrates had split,” explains Arendt, “But then found vertebrate—type hormones in annelid worms and molluscs, indicating that these centres might be much older than expected.” Comparisons of two types of hormone-secreting nerve cells from zebrafish, a vertebrate, and the annelid worm Platynereis dumerilii, in Arendt’s lab have now revealed some stunning similarities that point to a shared and ancient ancestry for our hormonal systems.

“These findings revolutionise the way we see the brain,” says Kristin Tessmar-Raible who carried out the comparison, “So far we have always understood it as a processing unit, a bit like a computer that integrates and interprets incoming sensory information. Now we know that the brain is itself a sensory organ and has been so since very ancient times.” The research appears in detail in the journal Cell.

Bewildering to think that I used to skewer these little creatures on a barbed hook and cast them into the sea to catch scaly marine creatures. It almost makes no sense.

Burying Carbon to Save the Planet

Recent research has highlighted the possibility of burying, or sequestering carbon dioxide in deep, disused coal mines. Not only might this allow us to reduce atmospheric carbon dioxide levels but the process would displace usable methane (natural gas) from the coal and extend the length of time we will have this resource available to us as a fuel and chemical feedstock.

However, I felt that the while the concept sounds viable initially, there are several loopholes in the whole carbon burial argument, especially when releasing methane is also brought into the equation. I asked team leader Thomas Brown of the US Department of Energy’s National Energy Technology Laboratory about my concerns.

First the whole process will require its own energy supply, which will in turn release CO2, as well as being expensive to undertake in practice. Moreover, most of the methane retrieved in this way will end up being burned as fossil fuel and adding still further to the global carbon footprint.

“You are correct,” Brown told me, “Cost projections for CO2 sequestration indicate it will be expensive and a great deal of research is currently underway to bring these costs down.” He points out the methane release process is quite encouraging because for every 2-4 units, or moles, of CO2 trapped, just one unit of methane is released.

“This suggests that [the process] has the potential to be more cost effective than the [alternative approach] of sequestration in deep saline aquifers,” Brown adds.

The coal bed methane will certainly be useful nevertheless and Brown points out that CO2 released by burning it will in turn have CO2 capture systems in place. “It is an additional energy source that can be utilized instead of venting it from coal seams to the atmosphere,” he says, “it also provides some offset for the cost of sequestering CO2 – methane is much more detrimental to the environment as a greenhouse gas than CO2.”

He adds that sequestration in coal seams my not be a viable option owing to low permeability values and swelling of the coal itself, which he discusses in his research paper. “More R&D is required,” he told me.

Bad Apples, Colds and Echinacea

Echinacea - Photo by Bruce Marlin Recent media reports seem to have strengthened the case for using echinacea to ward off or treat the common cold. But, are they based on valid new evidence?

The LATimes [item no longer available by link] for instance, says researchers carried out an “analysis of 1,600 patients pooled from 14 previously published studies found that echinacea reduced the chances of catching a cold by 58% and shaved 1.4 days off the duration of a cold.”

The researchers who carried out this analysis point out that none of the previous trials was large enough to be valid, but somehow they attempt to give them new credence by mixing together the data from lots more dubious studies. One bad apple can almost certainly spoil the barrel, but throw together a couple of dozen bad apples and that barrel is going to be humming before the day is out, surely?

Meta analyses of solid double-blind, placebo-controlled clinical trials certainly can shed new light on old findings, but what they do not do is create new data points, they are simply a re-analysis of old results pooled.

Craig Coleman of the University of Connecticut whose team carried out the meta analysis, point out that none of the trials analysed individually were big enough to reveal the benefits of Echinacea. Somehow his new analysis of old data demonstrates an almost two-thirds reduction in the risk of catching a cold compared to a person not using Echinacea. But, how could that be, if those earlier trials succumbed to serious wishful thinking and the placebo effect, then the whole argument is in doubt.

Wallace Sampson, an emeritus adjunct professor of medicine at Stanford University School of Medicine is quoted as saying that because the methodologies of some of the earlier studies are so suspect, this casts doubts on the pooled result. Exactly.

The team also reports that of 800 products containing Echinacea they investigated, there are large variations in the quality, which part of the plant was used – flower, stem or root – and how much so-called active ingredient is present. In addition, they suggest that more work is needed to check the safety of the countless formulations available. Their warning echoes other studies that have pointed to toxicity problems associated with long-term use of Echinacea products, although admittedly some of those studies might also be considered invalid because of poor methodology.

So, should we run to our local herbalist on the off-chance that we might catch a cold or if you’ve already caught one quickly down a dose of Echinacea to “shave off” 1.4 days or runny noses and sneezing? I don’t think so, not unless you don’t mind putting up with a whole lot of bad apples.

DNA Network

Sciencebase was recently invited to join the excellent DNA Network and as such our genetics news feed is now being pulled by the network’s feed system. If I had been a little slower off the mark, I could have been site number twenty in the list, but when I joined I think I jumped in at #18. There are, at the time of writing, nineteen members, no DNAying it.

So, here is a quick random selection of fellow network members. The links will take you to the individual RSS feed for each site whereby you can subscribe (for free) and get some great and timely information on DNA and the latest happenings and business news in genetics and DNA research.

VentureBeat Life Sciences

Discovering Biology in a Digital World

DNA Direct Talk

Epidemix

The Daily Transcript

henry: the human evolution news relay (genetics)

Mary Meets Dolly

Genetics News

Microarray and Bioinformatics

Gene Sherpas: Personalized Medicine and You

The Personal Genome

All excellent newsfeeds, all focused on one thing, DNA. You can find links to the others, including Eye on DNA, the owner of which led me to the DNA Network in the first place, via DNA Network. I’ll do another round-up of the remaining members later.

YASSE – Yet Another Science Search Engine

A new global science gateway – I’m sure they’d prefer me to display that phrase in blinking bright green text on a red background, but I won’t – has been launched by the US Department of Energy (DOE) and the British Library. The aim is in “accelerating scientific discovery and progress through a multilateral partnership to enable federated searching of national and international scientific databases.” Yeah, okay. But, isn’t this just yet another science search engine portal? Apparently, subsequent versions of WorldWideScience.org will offer access to additional sources as well as enhanced features.

That’s what they all say. I’m sure it’s a very worthy search tool and would like to hear from Chemspy visitors who have tried it out and found its results useful/useless (del. as applic.)

Incidentally, the webmaster risks a duplicate content penalty because the two canonical forms of the web address (WorldWideScience.org and www.WorldWideScience.org) both return “200 OK”. One of them should have a 301 redirect applied.

Ptaquiloside Redux

Almost ten years ago, I wrote a feature article on the cancer risk associated with the bracken toxins known as ptaquiloside for ChemWeb. The article was updated and mirrored on Paul May’s Molecule of the Month website at Bristol University, and quite bizarrely still draws a few readers to the Sciencebase site via my byline on the article. I suppose the reason it is still popular is that it makes it to page on in Google should you search for the word bracken.

Anyway, this article occasionally triggers some rather interesting correspondence with readers. Most recently, John Nayler emailed me to ask whether or not toxic chemicals from bracken might leach into groundwater beneath bracken-infested areas. I had to admit I did not know, but a paper published recently in the journal Chemosphere (2007, 67, 202-209) discusses the microbial degradation and impact of ptaquiloside on soil microbes themselves, which sheds some light on the potential impact of this carcinogenic toxin.

Another of Nayler’s concerns regards whether or not bracken is not simply an unpleasant weed with a cancer risk associated with eating the “fiddle heads” (a delicacy in Japan), but whether or not landowners, whose land is infested with bracken might be liable for public health lawsuits should those with a right to roam on their land be exposed to bracken spores. The risk may be small but that never stopped an ambulance-chasing lawyer in the past.

Cancer Research UK has a FAQ on the cancer potential of bracken. Despite isolated ptaquiloside coming up positive in carcinogenicity tests a decade ago, the latest research, according to Cancer UK is that there is no risk of cancer associated with eating bracken fiddlehead greens. So, what about those spores. Studies have shown bracken spores to cause cancer in mice, but those mice were given a lot of spores and to extrapolate to human cancer risk is (death)wishful thinking. A walk among the bracken is more likely to trigger a sneezing fit if the spores are high than anything else, and as CRUK points out, diet and smoking are far greater risk factors than bracken for cancer.

I Know What I Did Last Summer

This is what we were posting about a year ago this month, some of these are just plain silly, others are quite informative, but most just seem to lead to one thing on the mind:

Seat of Female Libido Revealed – Researchers found the organ in the brain responsible for female sexual response, I have to admit I hadn’t realized it had gone missing.

Keeping the lead in your pipes – Organs were being fiddled with in churches across Europe

Sperm and eggs – a sexy paradox…in fruit flies.

Erotic brain – Medical scientists discovered that women’s brains light up when they are exposed to erotic imagery, you don’t say?

Coca Cola Blonde – Yuck! (No Photoshop involved, by the way)

Beer vs wine – Beer is better, more B (vitamins)

I’m not sure if there is any kind of running theme here, (sex, booze…?), maybe it was just the time of year, the silly season was upon us, or you could probably even blame global warming.

Search on Steroids

Researchers at Xerox Corporation have developed new text mining software that goes beyond conventional keyword search, enabling it, in effect, to hone in on the one or two golden nuggets among the trash in the garbage pit. I asked the developers how applicable the system might be to science searching as it is originally aimed at administrative, legal and business type environments. Apparently, the FactSpotter software will be just as well matched to searching out elements of risk in scientific documents, for instance.

Is the Web Awake?

The web's awake A vast underground network exists in the American North West. The network is composed of the usual hubs of major activity with numerous interconnections, a complex packet-based communication system, and peer-to-peer sharing. But, this is not the familiar kind of network of BitTorrents, search engines, and wikis. This is a living organism, perhaps the biggest living organism. A fungus known as Armillaria ostoyae. we know almost instinctively that A. ostoyae is alive. It is an ordered entity, it assimilates nutrients and excretes waste products, it grows, it reproduces. Its metabolic pathways carry packets of chemical information along its network of tendrils. It exists beneath a 9 square kilometre area east of Prairie City in a remote corner of Oregon’s Blue Mountains at about 2000 metres.

So, asks Philip Tetlow in his latest book The Web’s Awake, can we similarly define the World Wide Web as being somehow alive, and more philosophically, aware?

Seemingly not. Tetlow draws together a network of evidence but comes to no more solid a conclusion than we cannot yet know whether or not the Web is awake, aware, or simply awash with random clusters of information and interlinks. His title would imply that he had evolved an answer to one of computing’s quintessential questions, can a true Turing machine exist? If the Web were awake, then it would be as parasitic as any fungal sprawl. But, it not only feeds on us, it offers us a symbiotic relationship in which we feed on its digital gifts.

The Armillaria ostoyae network would not exist if it were not for the roots of its forest host, but we still feel it to be alive. In the same way, the Web would not exist without the information and power we feed it. Nevertheless, we do not feel that the Web is alive. Of course, we do not yet know what future structure and organisation may emerge within the Web, maybe its offspring will be autonomous, a parasite or symbiote, maybe it will feed on us just as A. ostoyae feeds on the forest above and will ultimately destroy it.

There are no straight answers to Tetlow’s questions. Maybe we should JFGI. Just Flipping Google It!