I am interested in the information that is lost as scientists proceed from experiment to publication. The real factors that slip through the cracks of expediency. What is more important in the communication of research, the method, or the factoid results that come from it? Are we too trusting in the scientific method? Has peer-review become a substitute for a wider interrogation of method?
These are just a few questions going through my mind as I read "Simplification in Scientific Work: An Example from Neuroscience Research" - a 1983 article by the late Susan Leigh Star. I was particularly struck by an early observation in the article that "published scientific conclusions tend to present results as faits acomplis, without mention of production of decision-making processes." I am not sure that this is so true today, but I am intrigued by the possibility that it is exactly that loss of information (as research is presented with a higher degree of 'granualrity') that opens a door for skepticism in the wider community. When a large body of research by multiple scientific schools tends to agree on a matter, there is sometimes an impression given that they are all doing exactly the same experiments. Whilst the broad methods are the same, of course expedient decisions are made and this causes subtle differences. These are not always thoroughly explained, even if they are justified. I can't help but think that something in this is relevant to the skeptical program in climate change. Is this what lets in the calls of "conspiracy"?
More to read, more to do. I have a few other things on my plate, but this is an intriguing line of research.
Showing posts with label science. Show all posts
Showing posts with label science. Show all posts
Friday, September 3, 2010
Friday, February 5, 2010
For a brief moment...
You sit on the beach and grasp a handful of sand. Peering closely, you focus on one tiny grain. It is small, white and smooth. Bringing it closer to the eye, you notice tiny worn ridges and grooves, with even smaller silty grains in between. It's quite unremarkable, this miniscule grain with its infinitesimal debris. There must be a million million just like it that you have ignored. Yet you examine more closely. Soon you see the variations in colour, remnants of its glorious sovereign existence before being lost in the morass. You inspect the variation in form, the undulations in its structure. Fraction by fraction, this cubic millimetre of Earth reveals itself to you, and begins to tell you a story.
It is a very long story. It is an account no campfire could contain. Where it begins is only part of the tale; a part shrouded in the error bars of science, clumsily approximated by crude machines. To start at the finish is the only option on hand. How did it arrive at you feet? You look at the sea, the surf lapping at your feet; the sand in constant flux; insight creeps in, the dawn of new understanding. There are many grains twirling around. Some of those scratches and striations are now explained – it has been a rough ride for this crystal of quartz, knocked around by a thousand waves.
Looking further afield, you notice the froth of a longshore current, battered by the surf, interrupted by rips. There is movement there, and it comes along the beach. You and your grain of sand walk against the flow, constantly aware of the opposing flow only meters offshore. Suspended sand swirls in the breaking waves and the turbulent water heaves. As the surf gets choppier, you find yourself at an entrance where muddy water surges out into the deep. It is a river, and it is flowing. The water is not clear, clays and silts cloud the current and obscure the ripples of sand beneath. You look upstream; it stretches out into a vast estuary, the hills and the headwaters in the distance. You cannot follow this grain's prior journey any further; already you are far from your car, far from the comfort of civilization. Whence did this miniature grain originate?
Having walked the length of the coast to the river, you have reversed perhaps the most recent decades of the grain's history. The span of time reaches back far, far further than that. You have merely glimpsed a small episode on a diminutive stage. Were you to travel upstream, you would begin to grasp the forces at work. Look again at that grain. It is translucent in the light, a shimmering signal of its illustrious past. Underneath the craggy exterior lies a former glory.
Travelling upstream, you would find larger grains with the telltale reflectance of partially worn crystal faces. These are your grain's younger cousins. Quartz is very tough; a great deal of abuse is required to wear down a noble crystal face. There would be other grains too, of different parentage. Feldspars, birefringent, coloured with earthen hues; flakes of mica, sparkling in the sunlight, flittering away in the flow. You have travelled back in time, seeing your grain in younger days, perhaps a thousand years ago.
Climbing the shores, boarding an all-terrain vehicle, you traverse the steep slopes of an increasingly incised valley. Returning to the bank, you see not sand, but pebbles, and boulders, huge, lumbering hunks of rock. Immovable for man, toys to the forces of nature. Focusing closely at a rounded stone, you are struck with the diversity. All the cast is there, but in varying states of disrepair. The feldspars are softening, the micas peeling off. But there, there like glass, is your quartz. Steadfast in adversity. Rubbing your finger over the specimen, crystals of quartz fall into your hand, splendid crystal faces twinkle in the rays. You are close to the source. Ten thousand years.
Gazing further up, you can see the granite dressed hills of the headwaters. You are drawn inexorably towards the majestic vista. Hiking boots on, you tramp up the slopes. Here, in the furthest reaches of this guiding stream, you find a large rock face. It shows its age, the skin peeling like an old onion. The crumbling face reveals beautiful perfection beneath. A batholith, older than the very hills it supports. Drilling in, you retrieve a core of sparkling granite. There, there in that smooth exposed surface, you see the players in their heyday, ready to act out the next scene, anticipating an audience. Yet there has been a pause. Time frozen in the act of crystallization. The quartz crystals are perfect, the feldspars lustrous pink, dark mafic minerals teasing for identification. You are at the chrono-crossroads, where time has stood still. This rock has been like this for six hundred million years, waiting unwearyingly for the next act. Pushed and heaved through the Earth, your grain's distant cousins have remained firm, with only the slow decay of atoms for company.
Before even that ancient crystallizing moment, those grains had another story to tell. Granite to migmatite, migmatite to metamorphosis; metamorphosis to diagenesis, and then on to sedimentation before one day, on a beach, near a river … it is a story for another day. We have reached back some half a billion years, and yet there is another four billion to go. Cycle upon cycle, these minerals have seen it all. They will see it again. How privileged we are to comprehend the journey for but an imperceptible stretch of time.
It is a very long story. It is an account no campfire could contain. Where it begins is only part of the tale; a part shrouded in the error bars of science, clumsily approximated by crude machines. To start at the finish is the only option on hand. How did it arrive at you feet? You look at the sea, the surf lapping at your feet; the sand in constant flux; insight creeps in, the dawn of new understanding. There are many grains twirling around. Some of those scratches and striations are now explained – it has been a rough ride for this crystal of quartz, knocked around by a thousand waves.
Looking further afield, you notice the froth of a longshore current, battered by the surf, interrupted by rips. There is movement there, and it comes along the beach. You and your grain of sand walk against the flow, constantly aware of the opposing flow only meters offshore. Suspended sand swirls in the breaking waves and the turbulent water heaves. As the surf gets choppier, you find yourself at an entrance where muddy water surges out into the deep. It is a river, and it is flowing. The water is not clear, clays and silts cloud the current and obscure the ripples of sand beneath. You look upstream; it stretches out into a vast estuary, the hills and the headwaters in the distance. You cannot follow this grain's prior journey any further; already you are far from your car, far from the comfort of civilization. Whence did this miniature grain originate?
Having walked the length of the coast to the river, you have reversed perhaps the most recent decades of the grain's history. The span of time reaches back far, far further than that. You have merely glimpsed a small episode on a diminutive stage. Were you to travel upstream, you would begin to grasp the forces at work. Look again at that grain. It is translucent in the light, a shimmering signal of its illustrious past. Underneath the craggy exterior lies a former glory.
Travelling upstream, you would find larger grains with the telltale reflectance of partially worn crystal faces. These are your grain's younger cousins. Quartz is very tough; a great deal of abuse is required to wear down a noble crystal face. There would be other grains too, of different parentage. Feldspars, birefringent, coloured with earthen hues; flakes of mica, sparkling in the sunlight, flittering away in the flow. You have travelled back in time, seeing your grain in younger days, perhaps a thousand years ago.
Climbing the shores, boarding an all-terrain vehicle, you traverse the steep slopes of an increasingly incised valley. Returning to the bank, you see not sand, but pebbles, and boulders, huge, lumbering hunks of rock. Immovable for man, toys to the forces of nature. Focusing closely at a rounded stone, you are struck with the diversity. All the cast is there, but in varying states of disrepair. The feldspars are softening, the micas peeling off. But there, there like glass, is your quartz. Steadfast in adversity. Rubbing your finger over the specimen, crystals of quartz fall into your hand, splendid crystal faces twinkle in the rays. You are close to the source. Ten thousand years.
Gazing further up, you can see the granite dressed hills of the headwaters. You are drawn inexorably towards the majestic vista. Hiking boots on, you tramp up the slopes. Here, in the furthest reaches of this guiding stream, you find a large rock face. It shows its age, the skin peeling like an old onion. The crumbling face reveals beautiful perfection beneath. A batholith, older than the very hills it supports. Drilling in, you retrieve a core of sparkling granite. There, there in that smooth exposed surface, you see the players in their heyday, ready to act out the next scene, anticipating an audience. Yet there has been a pause. Time frozen in the act of crystallization. The quartz crystals are perfect, the feldspars lustrous pink, dark mafic minerals teasing for identification. You are at the chrono-crossroads, where time has stood still. This rock has been like this for six hundred million years, waiting unwearyingly for the next act. Pushed and heaved through the Earth, your grain's distant cousins have remained firm, with only the slow decay of atoms for company.
Before even that ancient crystallizing moment, those grains had another story to tell. Granite to migmatite, migmatite to metamorphosis; metamorphosis to diagenesis, and then on to sedimentation before one day, on a beach, near a river … it is a story for another day. We have reached back some half a billion years, and yet there is another four billion to go. Cycle upon cycle, these minerals have seen it all. They will see it again. How privileged we are to comprehend the journey for but an imperceptible stretch of time.
Thursday, January 14, 2010
Grab More Science News Graph | LabGrab
This is a cool little app that gathers science news into categories. Worth a look...
Grab More Science News Graph | LabGrab
Posted using ShareThis
Grab More Science News Graph | LabGrab
Posted using ShareThis
Wednesday, December 23, 2009
Scientific method and "controversy"
There seems to be a common thread amongst sceptics out there that science is done via something that looks a little like the Council of Nicaea. That is to say, that a committee of scientists decides what is "doctrine" before instructing publishers what to print. There is confusion between the ways the legal system (or political system) works and how science works.
Lets have a look at some typical tasks in a scientist’s professional life:
1. Data collection. This can be the longest and hardest (and most boring) phase. This is where hours are spent over test-tubes, or, in my case, hours in the hot sun staring closely at rocks. Whilst you may be thinking about the end-game in this phase, the task is usually so routine that bias hardly exists (if it does, it is because the method itself is biased, or you're just sloppy). Actually, there will be mistakes, but these tend to revert to the mean, so will be cancelled out in the final analysis.
2. Hypothesis generation. I put this after data collection to bait some people, but actually, it has to be said that hypotheses are generated throughout the scientific process. The important thing is that you are only testing the original hypothesis whilst conducting an experiment designed to test that hypothesis. Other ones must wait for other experiments. There is no harm in "hypothesis-driven research" - this is what science is. However, this is different to biased research driven towards a pre-determined conclusion. Note the difference - a hypothesis is actually tested, a pre-determined conclusion is circular.
3. Data analysis. Here comes the statistics. So you have the data, and you see patterns. Are they significant? This is a technical, statistical question that determines whether you can use your data (gathered in 1. above) to test the hypothesis (2. above). If there is no significant result, then there is no support for the hypothesis from your results. THIS DOES NOT MEAN IT IS DISPROVEN. It is more like an absence of evidence, which, as the saying goes, is not evidence of absence. If the results show a statistically significant result, then you can compare it with your hypothesis. Now a hypothesis can be disproved - proposing that the sky looks blue and finding it to look green would be an example. Unfortunately the opposite does not apply. If your result concurs with your hypothesis, it lends support to it, but does not prove it. It can never prove it due to a quirk of inductive logic that demonstrates that no matter how many positive examples you show in support of a proposition, since the set of possible examples is infinite, you cannot rule out a counter-example emerging next. Which is quite different from the deductive logic of mathematics, where 2 + 2 = 4 as a result of the system itself.
To make a long story short, the last juicy step is publication.
Now you run into trouble. You've done your experiment, and supported your brilliant earth-shattering hypothesis. Will anyone believe you?
To find out, you detail your method (and the back story - why you felt it worthy of research) and your results and a bit of discussion on what it all means. Then you send it for peer review. This is a blind (well semi-blind - sometimes people work out who the reviewers are) process where your reviewer doesn't know who wrote the paper and is asked to appraise the science, comment, and put their opinion on whether it is fit to publish. Most papers fail this test on the first pass, and the majority never make it to publication. What tends to define success is that the paper details a properly conducted line of research taking into account previous work in a similar field. Failure in peer-review doesn’t mean that there is a conspiracy against you – it usually means your paper is either not relevant to the journal in question, or that you need to write up your science better. Without peer review, this statement cannot be made with any certainty about a paper.
Also, consider that how the media treats science is not the same as the science itself. Science is only balanced in its reporting in so far as it “objectively” reports the outcomes of research and the opinions of researchers. So 90% of scientists might agree with a broad-based position, but it only takes one from the 10% to balance a journalists report – giving a 50/50 impression. Note also the diversity of opinion that will lie within the 90% who agree – these people do not speak to a common mantra, they merely assent to certain generalisations.
So next time you see controversy about methods and "conspiracies" to promote one "side" of an argument over another, consider the above and consider that most scientists are too busy with the steps involved to also hold some sort of cabinet meeting on how to bend the entire scientific community. After all, that would be like herding cats.
Lets have a look at some typical tasks in a scientist’s professional life:
1. Data collection. This can be the longest and hardest (and most boring) phase. This is where hours are spent over test-tubes, or, in my case, hours in the hot sun staring closely at rocks. Whilst you may be thinking about the end-game in this phase, the task is usually so routine that bias hardly exists (if it does, it is because the method itself is biased, or you're just sloppy). Actually, there will be mistakes, but these tend to revert to the mean, so will be cancelled out in the final analysis.
2. Hypothesis generation. I put this after data collection to bait some people, but actually, it has to be said that hypotheses are generated throughout the scientific process. The important thing is that you are only testing the original hypothesis whilst conducting an experiment designed to test that hypothesis. Other ones must wait for other experiments. There is no harm in "hypothesis-driven research" - this is what science is. However, this is different to biased research driven towards a pre-determined conclusion. Note the difference - a hypothesis is actually tested, a pre-determined conclusion is circular.
3. Data analysis. Here comes the statistics. So you have the data, and you see patterns. Are they significant? This is a technical, statistical question that determines whether you can use your data (gathered in 1. above) to test the hypothesis (2. above). If there is no significant result, then there is no support for the hypothesis from your results. THIS DOES NOT MEAN IT IS DISPROVEN. It is more like an absence of evidence, which, as the saying goes, is not evidence of absence. If the results show a statistically significant result, then you can compare it with your hypothesis. Now a hypothesis can be disproved - proposing that the sky looks blue and finding it to look green would be an example. Unfortunately the opposite does not apply. If your result concurs with your hypothesis, it lends support to it, but does not prove it. It can never prove it due to a quirk of inductive logic that demonstrates that no matter how many positive examples you show in support of a proposition, since the set of possible examples is infinite, you cannot rule out a counter-example emerging next. Which is quite different from the deductive logic of mathematics, where 2 + 2 = 4 as a result of the system itself.
To make a long story short, the last juicy step is publication.
Now you run into trouble. You've done your experiment, and supported your brilliant earth-shattering hypothesis. Will anyone believe you?
To find out, you detail your method (and the back story - why you felt it worthy of research) and your results and a bit of discussion on what it all means. Then you send it for peer review. This is a blind (well semi-blind - sometimes people work out who the reviewers are) process where your reviewer doesn't know who wrote the paper and is asked to appraise the science, comment, and put their opinion on whether it is fit to publish. Most papers fail this test on the first pass, and the majority never make it to publication. What tends to define success is that the paper details a properly conducted line of research taking into account previous work in a similar field. Failure in peer-review doesn’t mean that there is a conspiracy against you – it usually means your paper is either not relevant to the journal in question, or that you need to write up your science better. Without peer review, this statement cannot be made with any certainty about a paper.
Also, consider that how the media treats science is not the same as the science itself. Science is only balanced in its reporting in so far as it “objectively” reports the outcomes of research and the opinions of researchers. So 90% of scientists might agree with a broad-based position, but it only takes one from the 10% to balance a journalists report – giving a 50/50 impression. Note also the diversity of opinion that will lie within the 90% who agree – these people do not speak to a common mantra, they merely assent to certain generalisations.
So next time you see controversy about methods and "conspiracies" to promote one "side" of an argument over another, consider the above and consider that most scientists are too busy with the steps involved to also hold some sort of cabinet meeting on how to bend the entire scientific community. After all, that would be like herding cats.
Dawkins on "Elders with Andrew Denton"
I am hardly the first person to examine the interview with Richard Dawkins and come out a little surprised. It has had a small rash of internet discussion, but being an Australian interview, has not yet captured the crazy creationist ire. Mostly it appears that neither Dawkins nor Denton did enough research on each other. This would have been an easier task for Denton than Dawkins given the quantity of material out there on Dawkins' views and indeed his life. Denton is less famous outside Australia and has a career in journalism and TV making him perhaps more adept at only letting out what he wants. Either way, as one person said to me, Dawkins looked at Denton as though Denton was from Mars at some points throughout the interview. Denton's style is usually to try and wrong-foot interviewees into revealing more about themselves by asking old-hat questions in unexpected ways. He triangulates on people, and it usually works, making him one of the best interviewers I've ever seen. Unfortunately, when faced with a person who is professedly largely ignorant on topics outside his own field, this tactic fails. This is what has happened with Dawkins' interview. A very straight bat to Denton is a good form of defensive play. In fact I had never seen that weakness until this interview.
Dawkins has been accused variously of being ivory-tower-dwelling, arrogant, pompous, strident (one he is particularly fond of) and narrow minded. However, this interview made Dawkins look humble when he explained that he doesn’t think that people should be interested in him, but that he does want to contribute his scientific knowledge to the world. His ideas about the value of truth and evidence I think were profound in the sense that rarely do people talk about it like that – the distinction between his views about life on other worlds versus the tooth fairy (or god) were very interesting. Perhaps he is right about the influence of fairy tales on children to prime them for religion. At no point did he distinguish himself from anyone else or make himself seem superior to others. Which is interesting considering that is precisely the sort of accusation frequently levelled at him. I think he did a good job of elucidating the difference between “belief” and “faith” and even distinguishing between religious faith and the kind of “faith” a scientist has in another scientist.
No doubt those who don’t like Dawkins will hold that up as an example of a boring, nerdy man who wants to take Christmas and tooth fairies away from children. Which is a shame since that is not what he said at all... And remember that Douglas Adams regarded him as a close friend, so he cannot possibly be humourless!
People seem incapable of grasping a central point to the philosophy of Dawkins and co. That is that there are seemingly infinite sources of wonder in the real world. There are new and exciting things to discover, and well worn paths to hold dear. There is little harm to be done in exploration, as long as a proper ethic is taken to the task. Not from god do we get to an ethics, but from analysis and reflection on life and its interrelationships. What is not known may never be known, but we do not yet know that! Wonder, beauty, love, happiness, suffering, these are all real things in the real world that do not require a heavenly explanation to make them worthy of experience. The methods of science have revealed to us much of which we would otherwise be ignorant. It is an ignorance that carries no bliss.
Perhaps Charles Darwin said it best, as he penned these words, a man no longer accepting faith, seeing instead a wonderful connection between natural processes over geological time and the diversity and beauty of life on earth:
"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."
Dawkins has been accused variously of being ivory-tower-dwelling, arrogant, pompous, strident (one he is particularly fond of) and narrow minded. However, this interview made Dawkins look humble when he explained that he doesn’t think that people should be interested in him, but that he does want to contribute his scientific knowledge to the world. His ideas about the value of truth and evidence I think were profound in the sense that rarely do people talk about it like that – the distinction between his views about life on other worlds versus the tooth fairy (or god) were very interesting. Perhaps he is right about the influence of fairy tales on children to prime them for religion. At no point did he distinguish himself from anyone else or make himself seem superior to others. Which is interesting considering that is precisely the sort of accusation frequently levelled at him. I think he did a good job of elucidating the difference between “belief” and “faith” and even distinguishing between religious faith and the kind of “faith” a scientist has in another scientist.
No doubt those who don’t like Dawkins will hold that up as an example of a boring, nerdy man who wants to take Christmas and tooth fairies away from children. Which is a shame since that is not what he said at all... And remember that Douglas Adams regarded him as a close friend, so he cannot possibly be humourless!
People seem incapable of grasping a central point to the philosophy of Dawkins and co. That is that there are seemingly infinite sources of wonder in the real world. There are new and exciting things to discover, and well worn paths to hold dear. There is little harm to be done in exploration, as long as a proper ethic is taken to the task. Not from god do we get to an ethics, but from analysis and reflection on life and its interrelationships. What is not known may never be known, but we do not yet know that! Wonder, beauty, love, happiness, suffering, these are all real things in the real world that do not require a heavenly explanation to make them worthy of experience. The methods of science have revealed to us much of which we would otherwise be ignorant. It is an ignorance that carries no bliss.
Perhaps Charles Darwin said it best, as he penned these words, a man no longer accepting faith, seeing instead a wonderful connection between natural processes over geological time and the diversity and beauty of life on earth:
"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."
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