Category: Biology

What is it with software and websites and scientific tools that they all have to have these mixed case acronyms, abbreviations, and odd spelling?

Anyway, today sees the launch of another odd spelling from the European Molecular Biology Laboratory’s European Bioinformatics Institute – CiteXplore. This is a freely accessible literature resource service that melds data from the peer-reviewed scientific literature with key biological data such as DNA and protein sequences, functions and structures of molecules and microarray data.

The tool essentially searches Medline abstracts, patent abstracts, and Chinese Biological Abstracts and links to publisher websites. But, the crucial difference between this and any other literature search tool is that it cross-links to EMBL-EBI’s biological databases.

‘When you are reading an abstract describing a specific gene or protein, typically you want more information on it, for example its sequence or its function, as well as easy access to the full paper,’ says Peter Stoehr, who coordinates CiteXplore. Built-in text-mining tools allow “touch of a button” or more aptly, “click-of-a-(lab)-mouse” access to the specific record for a molecule of interest.

This is just the kind of system that chemists Peter Murray-Rust and Henry Rzepa have been aiming for the chemical sciences. Once again, the bio guys seem to have stolen a march on chemistry.

Is it just me or is there a certain irony to be found in the timing of a rare cattle and other animal breeds conservation initiative being announced in the UK and stem cell researchers at Newcastle University requesting authorisation to hybridize nuclear-free eggs from cows with a human skin cell nucleus?

Ironic or not, both are issues that will inevitably attract great controversy over coming days.

The rare breeds initiative will build a database of livestock breeds across the UK to help. Announcing the launch of this genetic “Noah’s Ark”, the Department for Environment, Food and Rural Affairs sets out recommendations for how the industry and Government can improve and maintain the diversity of the UK’s livestock genetic material in the future. Among its detailed recommendations are the maintenance of an advisory body that better informs the public, industry and policymakers on the country’s farm animal breeds, the collection of high-quality information on genetic resources to provide effective ways for their future use, and support for the prioritisation, development and implementation of projects to conserve genetic diversity.

‘This plan is important economically, socially and culturally,’ says Food and Farming Minister Jeff Rooker, ‘We have a fine tradition in this country of breeding a diverse range of farm animals which in many cases can be found across the world.

‘However, there are growing concerns over genetic diversity as growing economic pressures have lead to a few specialised breeds spreading across the globe. The threat of exotic diseases is also a threat to diversity in some breeds.”

On the same day, scientists at the University of Newcastle upon Tyne sought regulatory approval to fuse an egg from a cow that has had its nucleus removed, with the nucleus of a human tissue cell, from skin for instance. The resulting hybrid, which would essentially be 99.9% human with only a tiny amount of mitochondrial DNA from the cow remaining. The egg could then be cultured and stem cells that are human to all intents and purposes, harvested from the growing chimera. The hybrid embryo would, the researchers say, be destroyed once the stem cells were collected.

They point out that human eggs are a precious and scarce a commodity, whereas there is a glut of cow eggs. Cow eggs are also a lot easier to handle than the eggs from the conventional source of laboratory test eggs, the mouse.

The UK’s Human Fertilisation and Embryology Authority (HFEA) is yet to grant permission although teams at Edinburgh University and King’s College London are also seeking approval for similar research.

The aim of creating such a human-cow hybrid is to develop the techniques that will eventually be used to create 100% human stem cells in the laboratory without having to expend years of human eggs honing the necessary skills that will ultimately make stem cell production routing.

Both strands of research, the genetic conservation program and the human-cow hybrid are already provoking a reaction from those who consider such efforts a violation of animal rights, another example of human exploitation of animals, and the lobbyists who want an outright ban on stem cell research.

Stephen Minger of King’s College London told journalists that, “We feel that the development of disease-specific human embryonic stem cell lines from individuals suffering from genetic forms of neurodegenerative disorders will stimulate both basic research and the development of new medicines to treat these horrific brain diseases.”

PS Before anyone says, yes, I know it’s a picture of a bullock not a cow and that, yes, you’d be hard pushed to extract cattle eggs from him, hybridised or not!

The world of online publishing continues to evolve and today marks a new landmark with the release on to the web of the complete works of one of history’s greatest scientists, Charles Darwin.

Every book, journal entry, and letter amounting to some 50,000 searchable pages and around 40,000 images from his original publications are now available to everyone with web access for free within a few mouseclicks.

Charles Darwin (1809-1882) revolutionized our understanding of life on earth and Darwin Online will revolutinize many people’s understanding of Darwin as well as bringing his findings to a much wider audience. The site represents the largest collection of his work ever assembled and allows users to search the complete text as well as view images of the original manuscripts in parallel. There are many documents that all but the keenest Darwin scholar will never have seen, including many previously unpublished transcriptions from his handwritten papers including the field notes from his seminal trip to the Galapagos islands.

Richard Dawkins told us in the 1970s that all organisms are nothing more than gene machines, robot zombies built by molecules we loosely know as genes to no end other than to ensure the replication of those very molecules. There is no purpose here, although Dawkins anthropomorphically endowed the genes with selfishness. Later, he extrapolated this concept of self-replicating entities to concepts, patterns of thought, that exist only in the organism we know as Homo sapiens and that are duplicated not by sex and reproduction but through communication via the systems we call culture. These self-replicating entities he referred to as memes.

It became apparent very early in the development of his meme theory that although a nursery rhyme or the concept that walking under a ladder may somehow bring one misfortune are persistent memes that can traverse the generations through repetition from parent to child and in playgrounds the world over, one meme in particular seems to have been with us since the beginning of human culture. The idea that there is a god, a creator, a supernatural entity that brought humanity and all the universe into existence purely for our benefit.

Dawkins believes this is a nonsense. Evolution teaches us that humans exist because as gene machines our ancestors were better suited to the environments they encountered and able to reproduce. Each one of us can trace our ancestry through a long-line of survivors all the way back to the Cambrian Explosion and beyond to the dawn of life on earth. However, consciousness brought with it the realisation of death, our emotional centres couldn’t cope with the death of loved ones nor the thought of our own mortality. It also brought with it curiosity about the very origins of the world and ourselves. Put the two together in the form of some kind of supernatural creator and the potential for this consciousness to persist after death and you have a good-feeling meme that explains everything and wards off the fear of death in one fell swoop.

Unfortunately, this simple meme, which may have seen our ancestors through many a dark night, spread and diverged into as many different forms as there are languages on the planet, so that today we have the Christian, Islamic, Hindu, Sikh, Juddaic, Neopaganist, Jeddist, etc version of this meme and all the trouble its interpretation brings.

Dawkins wants to set the record straight, there is no “God” of the organised religions. That god is as real as the teapot that orbits the far-side of the Sun, he says. In The God Delusion he attempts to persuade the believers that the very thing on which their faith is founded is nothing more than a self-replicating cultural entity going by the name of meme.

His thesis wins him no friends among the religious and the specifics of his argument are not always accepted by science (but that’s the way of science). But, at least he’s honest. The death of religion itself, Dawkins says, would free us from the prehistoric or at best mediaevel, attitudes and rules that have shackled us for generations to the notion of an afterlife for us and our loved ones. He sees much more purpose in the beauty of life itself without resorting to a benevolent creator.

If deleting this meme from the gene machines we know as Homo sapiens were possible, we might truly see the dawn of an age of rationality in which killing because one’s imaginery friend advised one to do so was no more.