Tag: Science

Field notes and the promise of science…

Read on below for my live-blog post on ‘Helga Nowotny on the promise of science’.

Live-blogging from the Nobel Dialogue conference was a new experience for me—the aim being to sit through a lecture/dialogue, digest the information, write a coherent and constructive blog post and then publish before (or while) heading to next discussion. Despite some thorough research prep ahead of the first day, and reading plenty of live-blogging advice about battery power and staying hydrated, I managed to arrive in the auditorium totally dehydrated, and proceed to deplete my macbook battery in 90 mins. Thus, my first post was executed by mobile phone on WordPress for mobile and submitted by sacrificing my attention to the next talk. Fortunately, the nice thing about having a team other other bloggers is that you know they have the next talk covered.

Continue reading “Field notes and the promise of science…” →

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Telling tales…

The following is an excerpt about the current interplay between science and the media, taken from an article in this week’s Nature by Colin Macilwain:

…thanks to the massive growth in public relations and to online media’s insatiable appetite for ‘content’, journalism in science, as in other spheres, has evolved into an ugly machine — called ‘churnalism’ by media-watcher Nick Davies and others. This machine delivers inexpensive and safe content, masquerading as news, to an increasingly underwhelmed public.

The machine prospers because it serves the short-term interests of its participants. Editors get coherent and up-to-date copy. Writers get bylines. Researchers, universities and funding agencies get clips that show that their work has had ‘impact’. And readers get snippets, such as how red or white wine makes you live longer or less long, to chat about at the water-cooler.

None of these groups is benefiting strategically from the arrangement. Science is being misrepresented as a cacophony of sometimes divergent but nonetheless definitive ‘findings’, each warmly accepted by colleagues, on the record, as deeply significant. The public learns nothing about the actual cut and thrust of the scientific process, and as a result is beginning to adopt a weary cynicism that can only rebound on science in the long run.

Continue reading “Telling tales…” →

Spirituality…

I WAS in London last weekend (pics) meeting some wonderful people. One topic of conversation that came up late one evening was spirituality. It’s something that I have, in the past, had a lot to speak about. However, often pre-conceived notions of what spirituality really means (and we are well into in the realms of semantics here) hinder some discussion. This wasn’t the case the other day; as cursory as the discussion was, spirituality was not viewed as a skeptically-negative concept, but we were all way too tired, and the safe side of sober, for that discussion to last.

I’m re-posting an old post, written when I had something to say about the matter.

Thoughts?

Post, of the same name, re-posted from an earlier incarnation of this blog:

AMAZEMENT still strikes at our primitive emotions. When we are left in bewildered awe at a spectacle or new insight, it tugs at us in a manner that a reasoned scientific account can do no justice. It is, in many respects, a “religious” experience, but the word “religious” is bandied around in place of a slew of terms that could be used.

Such experiences are spiritual, being of matter (the brain still being a material object), yet insubstantial and deeply emotive. Whether it is some perception of a deity, or a new dimension of worldly understanding provided by science, these experiences are linked in their spiritual nature. In fact, I am with Carl Sagan in my belief that science is a profound source of spirituality.

In talking about spirituality, there is no implication of talking about religion. Spirituality is a sense of meaning (or purpose) and unity, but it does not have to be divinely inspired; it should not be confused with mysticism, which is concerned with magic, the occult and supernatural. The scientific journal Nature defines spirituality it as “An inner sense of something greater than oneself. Recognition of a meaning to existence that transcends one’s immediate circumstances”. It’s a good word, and one that we ought to take back, releasing it from its pre-scientific context.

Nature and the universe certainly put us in our place with the realisation that the atoms that make up your body are billions of years old, they’ve made many other things in their existence, and will continue to do so long after we’re gone; we are simply borrowing them for a while. Scientists, and readers of science, have a lot to be spiritual about. We have a particular impulse to understand the world around us. It is a great injustice to ignore the natural world in favour of an inferior and artificial facsimile in the form of the supernatural. Why ignore what is in front of your eyes, from the sub-atomic to the cosmos, and instead make it up?

Science doesn’t have all the answers, but it has more than any faith can offer me. Science has so many more questions that it will answer, whereas most faiths have said everything they have to say. Fortunately, as a rational human being, and a scientist, I don’t need anyone to agree with me to be comfortable in my reasoning. If a million scientists decided to recant on DNA being the basis of genetic inheritance, unlikely as that is, it would mean nothing. DNA would still continue to be the basis of genetic inheritance unless they had hard evidence to the contrary. It is this facility than enables freethinking, rational people to be truly uninhibited and unprejudiced.

So why is spirituality important? Science can, in a practical sense, only really deal with the material; though this “material” may extend well below the size of an atom, or may be as intangible as love or trust. We still inhabit physiologically stone-age bodies with minds hard-wired for day-to-day problem-solving, strategic planning and interacting with the physical world that our ancestors could see, hear, touch, smell and taste. Yet we managed to arrive at this state in the absence of both writing and mathematics. Most of what we’ve achieved since then has been achieved by co-opting these more primitive thought processes (the original “transferable skill” set) and applying them in a new direction: complex reasoning and abstract theoretical modelling, applied to science and mathematics.

It is no surprise, therefore, that much of what we have learned in science is difficult to process, especially when they are beyond the resolutive power our innate senses; we need things to have defined boundaries and exist at the right scale. We know there is a sense of change; that processes are shaping life, the planet and the universe around us. We are part of something shared, much greater than ourselves, and every time science offers a new awesome insight into this, we find a connection with our spirituality.

Productivity…

Productivity (Copyright Jorge @ phdcomics.com)

THE thing about being a practising scientist working in academia is that when such a practising scientist decides they want to write more about science in general, they remember that academia is a toxic gas that expands to fill all available space.

We might hope for reprieve from standing at the bench, just a small amount of time to get a handle on our writing, a quick moment to imbibe some of the multiple streams of information from emails, journal table of contents, RSS feeds; alas, the moment a window opens, it is filled with responsibility. This may come in the form of the help you promised someone when you next got a chance; or hunting down an expensive enzyme in neighbouring labs, of which you require a mere fraction of a unit for a throw-away experiment; it could be trying to find a journal article with some essential information, rather than one that is actually interesting. Alternatively, you may just sit and stare into space, your brain already so depleted of sugar that you are protocolling on auto-pilot.

Having filled your day with preparations for experiments, and the remaining 5% of it getting to finally do the experiments, you turn your attention to your student, who is working on a completely different project, with its own set of unique and inconvenient problems, and for which you must but don’t have answers.

Having finally left the lab, if you’re lucky, you’ll manage to get home in time to cook some award winningly simple food (credit us with some respect, some of us do cook from scratch), which is invariably eaten in front of the computer while you finally get to sift through the now ridiculously over-burgeoning information stream, which now includes – lucky me – about a million twitter entries and their links.

Ultimately, if you’re not ready to go by 2 am, you have two choices: either spiral into pit of information overload, eyes glazing over as the numerous ideas that pop into your head leave just as fleeting and unformed as they arrived; or sleep.

There are of course some researchers out there who do manage overwhelmingly with both their professional and private pursuits, hell, I even manage it myself sometimes. But right now, I need a week’s worth of sleep.

Lame theses….

[ratings]

Here is an excerpt of a philosophical lecture series going on at my institution:

The Mangoletsi Lectures 2009: God, Science and Philosophy
Peter van Inwagen, John Cardinal O’Hara Professor of Philosophy, University of Notre Dame

Lecture 4: God and Science II

I return to the topic of a possible scientific disproof of the existence of God. Unlike the discussion in the first lecture, this lecture considers a particular scientific theory in detail—the Darwinian theory of evolution. I give a statement of the theory, present some reasons for being skeptical about whether it is in every respect true, and present an argument for the conclusion that, whether the theory is true or false, its truth is consistent with the thesis that the universe was created by an intelligent being. Finally, I defend a stronger position than the consistency of the Darwinian theory with the existence of an intelligent creator; I defend the thesis that, if the Darwinian theory were true and known to be true, our knowing that it was true would not provide us with any reason to believe that the universe does not have an intelligent creator.

—

He takes a Papal line by stating, ‘I defend the thesis that, if the Darwinian theory were true and known to be true, our knowing that it was true would not provide us with any reason to believe that the universe does not have an intelligent creator‘.

His erroneous use of the phraseology ‘if the theory were true and known to be true‘ demonstrates a fundamental disconnect in this man’s understanding of science. What we can say is ‘the theory is not false, and has been shown (countless times) to not be false’.

What he appears to be saying is, if you can’t disprove the existence of God, then ipso facto, he exists. It is a tenuous, and rather Catholic, position he hopes to defend, that demonstrating the validity of the theory of evolution, as we have, does not give us any reason to believe there isn’t still an intelligent creator. You could just as soon state the opposite. Obviously the existence of God is not open to scientific testing as no testable hypothesis could realistically be formulated; however, we can (and have) amassed enough data to obviate a need for a God in the equation.

Obviously he’s left himself some wriggle room in the form of, ‘its truth [the theory of evolution] is consistent with the thesis that the universe was created by an intelligent being‘; yes, sure, if you want to fudge it into your own creation story go ahead. It could be consistent with whatever you like, feel free to merge the rigorous science with anecdotal and fantastic origins theory, but this does not give it any more meaning, you’re merely hand-waving on the bits for which you have no explanation, i.e. the origins of life (which evolution in itself does not describe).

Meanwhile scientists will continue to remain curious and investigate the actual origins, rather than making up answers.

In preparation…

[ratings]

ON Friday I fly to Melbourne, Australia, to visit my Sister who lives and works out there. I’m not fond of long haul flights, especially when I’m flying economy, but I am very excited none the less. The flight could go either of two ways: I may decide to relax and just watch hours of on demand films and TV, something I rarely get to do on a day to day basis; or I could write. I could write about all the things I’ve been meaning to write about, but haven’t for lack of time.

I wrote a short story in my head the other day about a woman with a huge mole on her nose. She becomes obsessed with it, and the fact that people stare at it all the time ( interestingly the topic of why we stare was covered in a recent article by Wired magazine). After a while the woman decides to have the mole removed, and she is left with a perfect nose, but now no-one stares at her any more. She find this really depressing, she feels alone and isolated, no longer the focus of any attention. Sometimes we surgically excise things from our lives that we think we hate, but in fact they turn out to be crucial to whom we are.

I’ve also been meaning to write about atmospheric microbiology, or aeromicrobiology; it’s a fascinating discipline studying the world in which microbial life surfs the jet stream high up in the atmosphere, surviving the extremely harsh environment: low pressure, freezing cold, low oxygen and high radiation. The Scientist magazine ran an interesting article on it some months ago, entitled ‘They came from above’, by science writer Brendan Borrell (Volume 22 | Issue 12 | Page 36; you can get it via Borrell’s clip archive).

Borrell describes a key event in aeromicrobiology as when Fred Meier of the US Department of Agriculture convinced Charles Lindberg to collect [air] samples during an Arctic flight from Maine to Denmark in 1933, where they found everything from fungal spores to algae and diatoms. Sometimes these wayward, or more appropriately ‘windward’, bugs are more serious that we give them credit. Borrell goes on to describe an outbreak of the [normally tropical] fungal pathogen Cryptococcus near Vancouver in 2001, where vets recorded 12 cases of Cryptococcus in domestic dogs, cats (and even Llamas). The outbreak dated from 1999 and a USDA APHIS report of it is available here, it makes for interesting reading.

The idea that this organism may have arrived on the wind, or may have been lurking in the valley, only for its spores to become airborne and ‘bloom’ in the hot summer of 2001, is understandably something worth investigating. Studies have identified links with atmospheric dust from North African dust storms bringing infectious and irritant fungal spores and allergens to Spain, and even as far as Barbados where one strain (Aspergillus sydowii) was found to be responsible for killing sea fan coral in the Caribbean (more detail about that event here).

Cases of wind-borne fever have been documented previously, in one case people in the populated areas of the Cote du Rhone region of southern France suffered from the zoonotic (i.e. from animal) disease Q-fever, caused by the bacteria Coxiella burnetii, borne the Mistral wind, the cool dry wind that blows through the South of France, from rural areas inhabited by some 70,000 sheep. Obviously there’s not a lot you can do about this, other than monitor such occurrences, but knowing more about it is a good start.

I’m sure there is a backlog of other articles and people I need to discuss, so in the next two weeks you will either see a photoblog of people and places in Victoria, Australia (taken with my new Sigma 10-20 mm lens), or a rather large body of writing. More likely it’ll be a bit of both, or neither; how’s that for clarity?

Anyway, returning to my impending trip, I still have a major experiment to get under way this week, which really does need to go well. I have a lot of man-hours invested in this, and it all essentially comes down to two sets of experiments, each looking for the same reaction to happen in two completely different environments. They’re fiddly, they can easily go wrong, and they’ll be labour intensive – not the best combination when really I should be deciding if I need to decide whether I should be taking sandals or warm boots to Melbourne in Winter.

So it goes.

The dead zone…

rb2IMAGINE that you’re walking along a path in the middle of a prairie, minding your own business. As you’re walking, you find yourself getting out of breath; you find you’re unable to exert yourself as you can’t seem to breath fast enough. Pretty soon you start becoming slovenly, slow moving, dulled; there’s something wrong with the air, there’s not enough oxygen; you’re in the ‘dead zone‘. You try to move away from where you are, but you don’t know where the bad air started. Before long, it’s too late.

A similar experience may happen to deep ocean fish. They need oxygen too, they just manage to get it from the water, but there’s a problem. A report in the April 17th edition of Science, by Peter Brewer and Edward Peltzer (Monterey Bay Aquarium Research Institute, Moss Landing) describes how ‘Ocean “dead zones” [defined as regions where normal respiration is greatly limited and the expenditure of effort is physiologically constrained], devoid of aerobic life, are likely to grow as carbon dioxide concentrations rise.’ In order to understand what their report is about, we need a little background.

Continue reading “The dead zone…” →

To whom are they selling…?

IN the past few years I have found myself on the receiving end of some fairly bizarre advertising campaigns from large biotech companies.

First there was MWG Biotech (as they were called at the time), who make short stretches of single-stranded DNA called oligonucleotides, which many of us use in our experiments. They decided to market these using cartoon characters, the chief of whom was ‘Olly Oligo”. This was the first time I asked myself, ‘who the hell are they aiming this at?’

Then we were assaulted with the extremely kitch ‘PCR Song‘ from Bio-Rad. Thanks for this guys, it took weeks to try and forget it.

PCR song
Bio-Rad's PCR Song

Then came Eppendorf’s ‘It’s called epMotion‘ music video for a robotic liquid handling station; a deliberately tongue-in-cheek boy-band styled affair, also available as a ring tone. I wasn’t swayed.

Eppendorf's epMotion boys
Eppendorf's epMotion boys

The most recent shockers, inciting this post, are from the Biotech giant Roche, who are marketing a means of monitoring cell cultures using electrical impedance measurements, xCELLigence. However, they’ve gone for a more obvious tack. They’ve done a rock video.

Roche's exCELLigence rock
Roche's exCELLigence rock

Actually, they loved it so much, they did a second rock video. Why do just one when you can have two videos for twice the price?

I’m actually now speechless.

The great divide…

[ratings]

IN geographic terms, the ‘great divide’ is used to define the point in the USA, roughly following the course of the Rocky Mountains, where on one side a drop of water will run down into the Pacific Ocean, and on the other, it will run down into the Atlantic.

There is however another great divide in the USA, which is between those that have a basic knowledge of the world around them, and those that don’t. The online newszine Science Daily described a recent poll commissioned by the California Academy of Sciences, in which a series of basic questions, designed to assess basic science literacy, were posed to 1,002 adults over a four day period last December. The poll has been ongoing (though in a less rigorous sense) online at the CAS website. The results were as follow:

  • Only 53% of adults know how long it takes for the Earth to revolve around the Sun [a year, 365 days]
  • Only 59% of adults know that the earliest humans and dinosaurs did not live at the same time. [Duh]
  • Only 47% of adults can roughly approximate the percent of the Earth’s surface that is covered with water. [where the answer of 65-75& was taken as approx. correct, though 15% gave the correct response of 70%]
  • Only 21% of adults answered all three questions correctly.[!]
  • Less than 1% of U.S. adults know what percent of the planet’s water is fresh [3%]

Hands up who thinks this is unacceptable?

No, it’s not. So why is the USA finding it has a problem with scientific literacy? Well, please just indulge me. Let’s think about Pakistan, where many (though not all) Madrassas (Islamic schools) are engaging in the indoctrination of a new generation of children into fundamentalist rhetoric; this comes at the cost of education that can raise people out of poverty and morbidity; education that gives them some control over their lives. However, for many, Madrassas are the only source of ‘education’. Yet if you speak to a young professional on the street of moderate urban centres such as Karachi, they are not going to present you with the fundamentalist hard-line; they are the lucky few, to have been born into a better area, perhaps to a richer family whom are well educated.

It is not such a great step to see such a partisanship developing in the USA, with the richer, well educated ‘elite’ being outnumbered by those who are disenfranchised from modern successes, scientific discoveries and societal benefits. Those left behind in progress increasingly turn inward toward timeless stalwarts such as the fundamentalist hard-line, which not only serves to widen the gulf to be crossed by communicators of science, but ultimately results in senators, congressmen and governors becoming willing to bow down to public anti-science opinion, i.e. votes, at a government level, thus jeopardising the future scientific and medical progress.

Continue reading “The great divide…” →