Mental Indigestion

by Jim Caryl

Category: Philosophies

Changing your beliefs…

FOLLOWING on from my post yesterday regarding people’s concept, or lack thereof, of evidence, it was suggested that it would be an interesting thought experiment for those of us who are willing to offer criticism on a subject to put ourselves on the receiving end. I think it’s a good idea to find something that each of us holds dear or true, and see if we can challenge ourselves to imagine how we’d feel if someone argued against that view. By understanding this, perhaps we can better approach our means of approaching such as subject with someone for whom such criticism would represent a paradigm shift.

As I managed to shake silly beliefs such as ghosts and ley-lines as a child, the only examples I have as a thinking adult are with particular scientific hypotheses that I’ve subscribed to, but subsequently had to ditch. This is the general method of science, and in my own research there have been any number of hypotheses I’ve formed and subsequently disproved on the basis of new evidence.

However, there have also been explanations for some natural phenomena that pre-date my research career, and to which I subscribed whole-heartedly. One example dates from my time as a first-year undergraduate studying marine biology. I had a particular interest in marine invertebrates and once attended a lecture by Donald Williamson, who was the major proponent of a larval evolution hypothesis, and recently came to light as being accused of ‘fringe science’ and getting a paper in the Proceedings of the National Academy of Sciences (PNAS) under the radar; thus also highlighting the pitfalls of the ‘I’ve got a mate in the club’ attitude to publishing.

Essentially Williamson felt that the immature forms (larvae) of many such invertebrates can be thought of as distinct organisms from the adult form, which are often comprehensively different both physically and physiologically; think caterpillar to butterfly, or blobby polyp jellyfish to its adult ‘medusa’ form.

Williamson felt that these different forms arose through hybridization — the fusing of two genomes (of two distinct organisms), one of which is now expressed early in an animal’s life, and the other late.

You can read an Sci. Am. article about it here.

I have to say, I absolutely LOVED this hypothesis, it was very exciting and I lapped it up with the typical fervour of an undergraduate.

Trouble is, since then it has been rebuked often and has not been substantiated by the experiments that were performed to test the hypothesis. I was quite recalcitrant about such rebukes up until the most recent PNAS rebuke that I’ve just linked to.

You can read rebukes to the Sci. Am. article here.

Changing my view about this hypothesis was hard, and a little embarrassing given I so animatedly communicated it to all my friends until I learnt it didn’t have strong grounding.

This is very true of many areas in which we are not experts, whether you are a scientist or not, and the fact is that we do tend to confer a great deal of trust in some individuals depending on their position. I would add that Donald Williamson was not ‘wrong’ to form this hypothesis at that time; scientific knowledge is by its very nature transitory, but once it has been tested, and alternatives developed, then we should seek to move on.

I could have easily ignored the evidence that Williamson’ hypothesis did not hold up to, and continued telling people an interesting and captivating story about why adult and juvenile forms of invertebrates are so different, but I didn’t. There’s still a part of me that thinks that there may still be something in it, which is why I can relate – to a point – with those people facing their first reality-check with regards some pseudoscience that they’ve hitherto believed in.

Donald Williamson is now retired and still stands by his hypothesis.

I don’t.

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.

Risk taking and audacity in science…

Research bloggingIn the October edition of Cell1, Amy Maxmen, a New York based science writer, discusses how tackling long-standing scientific problems (i.e. studies that have been prone to failure), or refuting dogma, are perceived to be a poor strategy for early-career researchers; and contends that perhaps they shouldn’t be.

One of the reasons for this is down to the policies of research grant committees.

A common complaint among researchers is that in order to be funded, they feel they must submit conservative grants filled with so much preliminary data that their predictions aren’t quite predictions any more. As Venter says, “The problem in [grant] study sections is the philosophy of proposals being reviewed as contracts instead of ideas.”

My own thoughts are that sometimes the amount of preliminary data required in a grant submission is so great that you’re half way to addressing the research goals at the first base, but only at the cost of the remnants of the last grant, which were used to finance the preliminary studies for the next. It’s as if the research councils are looking for a sure thing, a guarantee of success.

This is not how science should work.

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The science inside…

Research bloggingA THESIS in the current edition of Nature Nanotechnology addresses the tricky minefield of scientists’ objectivity; the premise being that, on the basis of several lab studies carried out by social scientists, science is more subjective than many scientists realise.

Such lab studies stem from the desire to understand the creation of scientific knowledge from within the scientific community, which is certainly a worthwhile subject of study, but then again, if you were to walk into an operating theatre halfway through a bowel resection, you might think they were actively butchering the poor patient. I would thus err on the side of caution before leaping to conclusions about the validity of science on the basis of such sociological discourses.

There is this rational scientific ideal where, in order to be as objective as possible, we withdraw from our personal identities (nationality, gender, religion), thus diminishing our individuality and, consequently, our subjectivity. This of course sounds like a lab full of robots, and frankly the idea of working in a lab with a bunch of emotionless, predictable automatons makes me shudder. Then again, some of us do, and I’d love to hear how that works out for those people.

The thesis cites two influential pieces of ‘lab studies’ literature, both within high-energy physics: on one side (in Beamtimes and Lifetimes, by Sharon Traweek), it was revealed that scientific culture was replete with subjective cultural values and practices, yet Traweek concluded that,

good science can come from a lab even when various kinds of subjectivity are at work.

On the other side (in Constructing Quarks, by Andrew Pickering), this is contrasted by the conclusion that the scientific culture was so far removed from the ‘ideal of pure objectivity’ that,

the understanding of quarks developed by physicists was not to be believed because the science had been corrupted too much by non-scientific influences.

Fortunately, the thesis continues, most lab studies are closer to Traweek’s than Pickering’s, yet despite the differences in their conclusions, both studies address a mild concern of subjective values and practises.

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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.

Evolution of a scientific discipline…

[ratings]

Research bloggingTHE recent issue of Trends in Biochemical Sciences contained an interesting perspective piece from Alexander Shneider, PhD and CEO of CureLab in Massachusetts. He describes a revision, or alternative focus, of Thomas Kuhn’s (1962) theory of scientific (r)evolution. In this Shneider identifies four-stages of evolution through which a scientific disciple must pass to maturity:

Stage 1. The introduction of new objects / phenomena, with an accompanying language to adequately describe such phenomena.

Stage 2. Development of a ‘tool box’ of methods / techniques to probe the objects / phenomena; with advancements in methodologies helping to identify and understand the degree to which other phenomena fall into the realm of this new science.

Stage 3. The stage at which most of the specific knowledge is generated, with the majority of research publications being published, often focussing on the application of new research methods to objects / phenomena. Scientists may re-describe their subject matter using refinements from stage 2, in the same way that with the advent of molecular biology, biologists might re-describe old subject matter from this new context; thus creating new insights, new answers and new questions.

Stage 4. A seeming steady-state for a discipline, where the knowledge gained from earlier stages is is maintained and passed on, often with practical application; often with new means generated to present the information. Whilst ground breaking new discoveries are not necessarily made, this does not preclude crucial revisions to the role of this discipline within scientific environment.

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Open mindedness…

THERE is a video floating around the interweb that has proven very popular since its release; it’s called ‘Open-mindedness‘, by a chap called Doug (aka Qualia Soup).

I have forwarded this to numerous friends whom I felt may benefit from this perspective, and also to people who find themselves on the receiving end of being called ‘close minded’, essentially for banal things such as not believing in ghosts. However, in several cases now, it has been pointed out that the video has some flaws. These flaws are not so much to do with the content, but are more to do with the speed at which these potentially new concepts and argument are played out. As such, there is a risk that they may miss their mark in precisely those people who would most benefit.

For my own reference, and for some of the people who I know haven’t quite gleaned what the video is getting at, I’ve written a  para-phrased version that can be read and digested at the reader’s leisure; basically, I’m spelling it out. The core material and structure is taken directly from the video:

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Three cups of tea….

[ratings]

A Pakistani friend of mine recently lent me a book called ‘Three Cups of Tea’. At the time I had absolutely no idea how famous this book now is, it’s been on the New York Times best sellers list for 109 weeks. Reading it has been a formative experience.

It is the story of Greg Mortenson who, in 1993, after a failed attempt on K2, wandered accidentally into a small Baltistani village in the Karakoram mountains. The name of the village was Korphe (Kor-fay), and his experience here would change his and, by dint of this, tens of thousands of people’s lives in this impoverished region of the North-West frontier of Pakistan. The kindness of the Korphe villagers, their willingness to give Greg so much, when they themselves had so little, truly humbled him; thus prior to his departure, upon seeing how the children of the village were forced to write their lessons in the soil with sticks, he promised to build them a school.

The book describes how Greg returned to California, broke and living out of his car, to raise the $12,000 required to build the school. From humble beginnings, to patronage by the late multimillionaire scientist Dr Jean Hoerni and the formation of the Central Asia Institute (CAI), Greg has directed the building of 80 schools, women’s community centres and student hostels in North-West Pakistan and Afghanistan. This could only have been achieved with a very loyal team of local contacts that Greg has a natural faculty to draw towards him. The schools are built by the people of the villages with the full support of the village communities.

The emphasis of CAI schools is on the education of girls, an idea captured by the maxim, ‘If you educate a man, you educate an individual; but if you educate a woman, you educate a nation’ (Mahatma Gandhi). This lasting and indelible educational structure is at the core of improving healthcare and welfare of villagers, but furthermore, will reduce the number of illiterate and uneducated people who would otherwise provide cannon fodder for radicalism by fundamentalist clerics; a mother is less likely to give her blessing to her son’s jihad, a strong social requirement, if she is educated and literate.

The byline of the book is, ‘One man’s mission to promote peace…one school at a time’. It is a noble cause and one that I will happily support. I highly recommend that everyone read ‘Three cups of tea’. If you enjoy the book, also read some of the CAI publications (Journey of Hope), which provide updates and fantastic photography of the current and ongoing projects.

The state of art…

If you take a photograph of art, is that art too? Or is it just a photo of some art? When does it stop being art? Do you have to manipulate the photo before it becomes art; a change in the original intended emphasis of message?

What about if you then take a photo of the photo of the art, does that then make it art? I think it might, but then why does taking more photos of the photos of the art make it more art than just the original photo; surely the latter is “closer” to the original artwork than the 2nd+ generation photo?

But then, is it the degradation and graininess in the 2nd+ generation photos that makes it artsy? Why, if the original artwork is degraded would this be more artistic? What would that mean for the original artwork? Was it not degraded enough, or are we now talking about something different? If so, where was the disconnect? Was it capturing the light of the art on a film or CCD? How is this different from capturing it on your retina? Is it the depth of field that makes the experience better, you can achieve this with a photograph; what if it is the smell?

Would it mean that the original artwork needed to be more degraded to be art?

I’m just a scientist tying to make matter do what it doesn’t want to do, but clearly it seems that art is doing what matters.

“Two plus two makes five” – Winston Smith, 1984.

IF enough people believe it, or if it is illegal not to believe it, will it be true?

I spend a lot of my time, probably too much, waging a battle of wits and reason with the truly and irredeemably unreasonable. The usual subject is the scientific theory of evolution. I preface the noun “theory” with scientific so as there is no mistaking exactly what we mean by theory.

Whenever I hear the words “Just a theory….” levied at a scientific theory, it sends a shudder down my spine. As I’ve mentioned before, and I will undoubtedly continue to do so, a scientific theory is not speculation or opinion, it is a comprehensive, logical and above all testable model that represents the best means of explaining the evidence. Furthermore it facilitates predictions that can be tested experimentally to continue to verify the reliability of the theory. The theory of evolution is just such a theory:

The theory of evolution explains that variation exists between individuals within a species, it explains how natural selection can act to drive this variation and it shows how, and describes why, some organisms display characteristics that make them better suited, i.e. fitter, for life in the environment in which they live. It explains how these “fitter” organisms are the ones more likely to survive and pass on their characteristics to offspring. It explains how, over time, these characteristics become a trait in all members of a species, and how less favourable characteristics can be lost. Ultimately, the theory of evolution explains how a species, over this long period of time and subject to much genetic change steered by natural selection, can be very different from its ancestors.

Now, the above paragraph is qualitative, and largely non-technical. However, bound up within the above is some impressively complex science. The debates that rage amongst scientists is not about the validity of the above, it’s about the specifics of how they’re achieved. Part of what I aim to do with this blog is not re-write any of the perfectly excellent books on evolution that are available, but to tackle those areas that are taken advantage of by religious fundamentalists. Science is a dynamic subject; by the time it is written up in a book, it is already out of date. As I mentioned before, there is a battle of wits going on out there, between scientists or other such rational free-thinkers, and religious fundamentalists (which for want of a better term, I call “Fundies”).
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