SciBlogs

Archive 2013

Fox News and GMO’s Michael Edmonds Dec 31

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I saw this clip on TV this morning (I didn’t realise what we see from Fox on Sky is a month old) and was “impressed” with the degree of muddled science and scaremongering they managed to put into such a short clip.

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inaccurate science (confusing viruses, bacteria with genes) – check

oversimplification of the science (“food made in a petri dish”) – check

overhyping/misrepresenting animal studies – check

conspiracy theories (“aren’t these people eating these foods?”) – check

typical poor reporting from Fox – check, check, check.

Sampling a Cell without Killing it – Nanobiopsies Michael Edmonds Dec 31

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I’ve just read a fascinating article in December 16th edition of Chemical & Engineering News* by Louisa Dalton which describes a new technique to sample cell material without killing the cell.

This new method, developed by biomolecular engineer, Nader Pourmand, and colleagues at the University of California, Santa Cruz, is able to withdraw approximately 50 femtolitres from the cell using a computer guided scanning ion conductance microscope. The computer guides a glass nanotube to the cell membrane where it is pushed 1 micrometre into the cell. A negative voltage across the tip of the pipette alters the surface tension between the cytoplasm and a solution in the pipette causing approximately 50 femtolitres of cytoplasm to be withdrawn from the cell.

This method allows cytoplasm to be withdrawn from different parts of a cell, with the cell remaining viable even after 10 punctures. The utility of this technique has been demonstrated by using it to extract and subsequently sequence, cytoplasmic messenger RNA from human cancer cells and mitochondrial DNA from fibroblasts.

This new technique opens the way to dynamic monitoring of cells. According the to the C&EN article “It permits many different types of measurements, such as single cell diagnostic tests or drug testing.”

* unfortunately this article currently appears to be behind a paywall.

 

Modern Medicine & Family Histories Michael Edmonds Dec 29

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Modern medical treatments, including vaccines, have helped extend life expectancies and quality of life through the prevention and treatment of disease. This fact is sometimes missed by those who oppose vaccines, criticise modern medicine and promote dubious “alternative” therapies. One reason for not seeing the benefits of modern medicine is that we take much of it for granted, and seldom see the effects of diseases of the past.

I have recently had the privilege of reading a family history of my great, great, great grandparents, James and Gerinia Ryan, and their descendants, put together by Eleanor Watt. It is fascinating reading, and also sobering when considering the deaths of four of their 15 children who did not make it past the age of 5.

George Edward Ryan died in July 1871 at 15 months of age from bronchitis

John Albert Ryan died in April 1878 at 13 months of age from deutitis (inflammation of the gums) and bronchitis

Jane Isabella Ryan died in June 1884 at 4 years of age from measles and pleurisy

Gerinia Eliza Ethel Ryan died in July 1884 at 9 months of age from measles and bronchitis

Critics of modern medicine often focus on diseases we have yet to find cures for, but in doing so they ignore the many successes – if born today the diseases which took these children’s lives are readily treatable.

I wonder what critics of modern medicine would find if they looked closely their family histories? How many relatives might they have lost to diseases now readily treatable?

The 10 “False Assumptions” of Modern Science? Michael Edmonds Dec 08

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Last week I came across a magazine I hadn’t seen before in Paperplus. Called “New Dawn” it purports to be “the No. 1 magazine for people who think for themselves” and covers a range of topics such as the afterlife, psychic healing with pets, astrology and conspiracy theories. Amidst this hodge podge of muddled thinking was an article by Mike Adams (aka the “Health Ranger”), who some readers may be aware of through their reading of other blogs such as Respectful Insolence.

In this article Mike Adams refers to the work of Rupert Sheldrake, who in his book “The Science Delusion”, criticises science. A while back I starting blogging about “The Science Delusion” however, after the first few chapters I gave up as the misrepresentation and misinterpretation of science was doing my head in (I swear I could feel the brain cells imploding in despair). Mr Adams in summarising Sheldrake’s key points at least makes it a less prolonged (albeit a still painful) process to respond to these supposed 10 false assumptions of science, as follows.

1) The universe is mechanical

Adams (based on Sheldrake’s writings) complains that modern science

“believes that the entire universe is made up of “stuff” and  nothing else. There is no consciousness, no spirit, no mind and nothing other than mechanical and chemical stuff.”

Of course he (they) have overlooked the existence of energy and the perfectly reasonable assumption that what we experience as consciousness (or mind or spirit) is simply a complex interaction of matter and energy.

2) All matter is unconscious

There is no evidence that matter itself is conscious, but this does not preclude the development of a larger consciousness as I have implied in my response above. Adams argues that

“modern science assumes humans are nothing more than biological robots” and

“the idea that inanimate objects such as minerals or crystals might have some sort of consciousness is considered heresy by most modern scientists”

I think the first statement is incorrect, while the second is correct and rightly so as there is no evidence to indicate to the contrary.

3) The total amount of matter and energy is always a constant

The disagreement with this “assumption” seems to be around the authors need for a creator/ grand designer etc and draws on unclarity around dark matter.

4) The laws of nature are fixed.

Adams refers to early theories (and examples?)  about faster than light  teleportation and quantum entanglement suggesting that these

“ignore(s) the apparent laws of physics”

The use of the word “apparent” seems quite ironic in that it almost hints that Adams realises, but refuses to acknowledge, that science does adapt its theories and even its “laws” when evidence to the contrary is provided and a better explanation can be formulated. Science is not the rigid framework he attempts to imply (of course if one wants to look at rigid frameworks of belief, one need not venture far from the dubious treatments such homeopathy, reikki and crystal healing that Adams is more than likely to support).

5) Nature is purposeless, with no goal or direction.

Criticism of this “false assumption” is based on the opposing contention that there is a “driving creative force” in nature which the author links to the concept of “spirit” and relies on criticism of Darwinian natural selection and misguided claims that there are no fossils of a “missing link between humans and primates.

Again, I would contend that while nature itself can be viewed as purposeless, sentient creatures, e.g. human beings can create purposes themselves and decide on their own goals and directions.

6) All biological inheritance is material carried DNA

This argument uses epigenetic factors, something well understood by modern science to argue that views of “old school science” that DNA alone controls your health, behaviour, and all your inherited attributes. I don’t know who these “old school science” beleivers are but I am not aware of any scientists who believe that DNA dictates everything around us. It has been quite clear for at least several decades that environment affects us, with epigenetics providing some of the explanation for us.

The trouble with many of those who claim this “false assumption” is that will often carry it too far in the opposite direction claiming that our genetic background has little affect of our health for example, and simple modifications of diet can cure ALL disease.

7) There is no such thing as a mind other than an artifact of of brain function

This is simply a rehash of points 1, 2 and 5. It seems to me analogous to claiming that a computer programme is an artifact of computer function.

8) Memories are stored chemically in the brain and disappear at death

I’d like to see proof that this is not the case beyond the authors suggestion that he is

“convinced that memories are holographically stored across not only the brain matter itself but also in a non-material spirit matrix of some sort which interacts with the brain”

9) Unexplained phenomena such as telepathy are illusory

Evidence please to show the contrary?

10) Mechanistic medicine is the only kind that really works

This section has some dreadful misrepresentations of modern science including statements such as

“most modern-day scientists do not believe that any vitamin, any mineral or any food has any biological effect on the human body other than providing calories, sugars, protein, fibre and fat.”

Talk about setting up a strawman. It was modern science that showed the importance of vitamins and minerals in protecting against a range of diseases. What I suspect is that Mr Adams has a problem with modern science not being able to support, in good conscience, various claims that high doses of vitamins and minerals can cure all manner of disease.

It then suggests that

“the mechanistic model of medicine is an utter failure for human civilisation”

ignoring the many successes of modern medicine while simultaneously providing no evidence for the successes of “alternative” medicine approaches. If Mr Adams would care to provide evidence for one of his “non-mechanistic” treatments and put it up against the successes of quinine, penicillin and morphine, for example, I’d love to see the comparison.

 

These 10 “false assumptions” of modern science are little more than poor interpretations and misrepresentations of science. Rather than being the

“dogmatic, permanently pessimistic science”

described by Adams, modern science is, in actuality, creative, thoughtful and adaptive. Rather it is those who push “non-materialistic” treatments such as reikki, crystal therapies and homeopathy with scant evidence to support them who are being dogmatic. Furthermore, ask any scientist an modern science is not pessimistic – it inspiring and fascinating for those who take the time to truly understand what science is all about.

 

 

Problem Based Learning in Chemistry Michael Edmonds Dec 05

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One of the plenary speakers at the NZIC conference this week was Professor Tina Overton from the Chemistry department at the University of Hull. We were lucky enough to have Professor Overton speak to us several times and she is a strong advocate of active learning, in particular, problem based learning.

In her coursework Professor Overton provides students with open ended problems, for example, asking them to work out how much gold is in the world’s oceans, or how many keratin molecules are produced every hour. For such questions students are not allowed to consult Google and work in groups where they reason through the answers. They are not expected to provide the “right” answer, rather the point is, how they work through the problem.

For example to work out amount of gold in the oceans, they may be provided with the concentration of gold in seawater and the diameter of the Earth, but the rest is left up to the students to reason through an answer.

One of the reasons Professor Overton takes this approach is that our current education systems (both here and in the UK) rely largely on algorithmic thinking – students take a series of facts or numbers and plug them into a formula to get an answer, without considering the “bigger picture” or seeing that the answer they have produced actually means something. These types of questions also provide a meaningful context for who chemistry can be used to solve problems, and also reflects real science, when sometimes the best you can do is make a calculated guess and that the “right” answer isn’t always possible to determine.

Professor Overton also presented some interesting data based on interviews with chemistry graduates asking them how the skills they had been taught during their degrees compared with those they needed in the workplace. The results showed that while they felt well prepared by their university training in terms of content, they had not been taught enough of the “soft” skills (I really hate this term as such skills are not as easy as “soft” suggests). For example, they felt underprepared in terms of their presentation skills, ability to work in groups and even in terms of their practical skills. Furthermore, the data showed that in many respects these skills were more important in the workplace.

The work presented by Professor Overton stimulated some great discussions amongst those interested in chemical education at the conference so perhaps we will see a bit more active learning appearing in undergraduate programmes around New Zealand in the future.

A “GoogleMAP” of Microbes Michael Edmonds Dec 05

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This week I attended the 2013 New Zealand Institute of Chemistry conference in Wellington which was great. There were a some fantastic talks and probably the most memorable for me was a talk by Professor Pieter Dorrestein from the University of California, San Diego.

The title of the talk was “A GoogleMAP”-type molecular map of microbes – from culture to people” and describe his work using techniques such as mass spectrometry, sequencing and informatics methodologies to identify the molecules produced by microbes in the world around us. Because different microbes produce different molecules, identification of the molecules helps identify which microbes are present – something which could allow quick and effective detection of disease.
However, because there are a multitude of microbes around us, and they can interact with each other, this is quite a complex task, with huge volumes of data, hence Professor Dorrestein’s group is using informatics to interpret this data.

One of their current projects is mapping the molecular world in 2D, 3D and topographically. In one experiment they mapped the microbial populations topographically over two of his students – one male and one female. The presence of unusual molecules in the male student saw him consult a doctor and find out that he had an intestinal complaint which was easily remedied. A good, albeit anecdotal example of how this topographical microbial mapping might be utilised in the future.

This research is also a good example how multidisciplinary research is leading to fascinating discoveries with wide applications.

Does success in science correlate with an acceptance of uncertainty? Michael Edmonds Nov 17

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One of the challenges with science communication is communicating uncertainty, something that is at the core of science but which produces some confusion and frustration for the wider public who prefer definitive answers to life’s questions.

However, this morning as I read the book “Cells to Civilizations – the principles of change that shape life” by Enrico Coen, it occurred to me that in most science texts there is uncertainty – as a author builds an argument he often relies on statements that only become clear later in the argument.

“Cells and Civilizations” is written by a plant molecular geneticist, and his explanations in the first three chapters mainly describe biological processes, often with analogies using art. My background is chemistry, and my knowledge of art is not extensive, so as I read this book I occasionally find myself thinking

“That’s interesting … I’m not quite sure I understand it fully .. but I’ll keep reading until I understand it better”

Even the author early on suggests

“I would encourage readers with little or no scientific background to keep going if they encounter tricky passages, as the key concepts should sink in as they are repeatedly encountered.”

And because it is an engaging book with some fascinating ideas, I continue to read it, and as the author suggests  these initially unclear ideas/examples are starting to make sense.

However, I can’t help but wonder if this need to accept that one may not grasp the full story straightaway (i.e. accepting a level of uncertainty) is what puts some people off science (and quite possibly some other areas of academic study)?

 

Appreciating Science in School – What to include? Michael Edmonds Nov 15

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In my previous post, I discussed teaching science in schools in terms of science and society, an idea that has previously been promoted by Sir Peter Gluckman.

So what content would be appropriate to include in such science and society/appreciating science curriculum?

I think you would have to include critical thinking/the scientific method at the core (something I believe has already been included in the latest redesign of the NZ science curriculum).

From my perspective, as a chemist, you would need to include:

atomic structure, a simplified description of the Periodic Table and chemical properties, contextualised perhaps by looking a a range of important elements, basic carbon chemistry perhaps related to plastics/proteins

In biology – basic cell structure, evolution …..perhaps some of our resident biologists could add to this, and perhaps physicists could do a similar list for physics?

Though it strikes me, that I have almost from the onset, instinctively separated science into the three historical disciplines. Is this the best way to go or should we teach science as a whole, and also pull in some history as well. I know it was the history of science, as shown on the TV show Connections, which got me hooked into science.

And are some schools doing this already?

Thoughts?

 

 

Appreciating Science* Michael Edmonds Nov 15

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Not everyone is good at science … and that is okay, can you imagine what it would be like if everyone wanted a career in science? However, this doesn’t mean that everyone cannot appreciate science, in the same way that I have developed a deep appreciation of music despite being tone deaf, and unable to play any musical instrument.

So how do we develop a greater appreciation of science?

For school students, I think more exposure to topics on science which focus more on science, society and critical thinking is the way to go. And this needs to be done from an early age. Science for problem solving, not memorizing endless facts, or doing meaningless calculations.

For the wider public, more public science events, particularly of topics of public interest – for example, Mark Quigley’s talks on earthquakes were attended in numbers more often seen at a popular rock concert.

Recently, I have developed a great (bordering on obsessive) appreciation of music/theatre, primarily because I am regularly exposed to the the most amazing performances by our students in the National Academy of Singing and Dramatic Art (NASDA). And this I think is an approach that will work for science – regular occurrences of high quality events will slowly capture more interest in science. We already have some fantastic events in New Zealand, for example, Otago’s Science Teller festival. We need stronger interactions between the primary, secondary and tertiary education sectors. And we need scientists to keep blogging, writing for newspapers and other outreach activities.

*Note – when I say “appreciating” science, I mean doing so critically. We need to recognise, as a society, that not all applications of science are necessarily good, and this can only be achieved with a scientifically literate society..

LENR and the Scientific Community – my perspective Michael Edmonds Nov 09

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One of goals of science related blogs is to encourage enthusiasm about science. However, sometimes this enthusiasm can be misdirected, for example, when people such as intermittent poster Derek Syms/Electrickiwi misunderstand the scientific communities reaction to areas  of research such as LENR (low energy nuclear reactions), also known as cold fusion.

Derek often makes demands that the scientific community should be doing more research in this area and claims this perceived disinterest is due to cover ups and corruption. I’ve written this blog article because I think such claims are worth unpicking in order to better explain how science works.

However, a good starting point is for me first to consider my own position on LENR. Science is not often as simple as being “for” or “against” a particular idea – it is about deciding what you think the best interpretation of the evidence that is available.

LENR/cold fusion first came to the public and the wider science communities attention in 1989 after Stanley Pons and Martin Fleischmann revealed their preliminary observations of an experiment which appeared to release anomalous amounts of excess heat, and suggested that it might be the result of nuclear processes which could potentially be a source of cheap, sustainable energy. Unfortunately the release of these results directly to the media prior to peer review and publication was not looked upon well by many in the scientific community and when there were difficulties replicating the work in other laboratories there was a lot of criticism of these two researchers.

Since 1989, a number of researchers have continued research in this area, now often referred to as LENR , and there is still debate about the nature of the anomalous heat produced. There are those who contend that it is a genuine phenomena, while others suggest that it is arising due to mis-measurement of the energy input/output or due to other problems with the apparatus.

Not being an expert in this area, I am happy to accept that there might well be a genuine phenomena here, but it seems to me that there just isn’t enough evidence to conclusively prove that this is the case, or that it is nuclear related. Nor is there any evidence that, should this phenomena exist, that it can be applied to the benefit of humankind – if the amounts of energy are so hard to measure that there are debates over whether it exists or not, I fail to see how this could benefit us.

However, I quite willing to be proved wrong (with scientifically verifiable evidence).

Another reason I am skeptical about the existence and potential applications of LENR is that research has been carried out for almost 25 years and there has been little advancement in understanding. It has been my observation that when a unusual idea is first discarded and/or laughed at by the wider scientific community, the proposers of the idea usually are able to provide enough evidence within a few decades to have it reconsidered and accepted by the scientific community – this does not appear to be the case with LENR.

In suggesting that the scientific community should do more research into LENR, Derek also overlooks the realities of doing scientific research. Funding is not unlimited (unfortunately) and there are a wide range of research subjects which can benefit humanity. In terms of our energy needs it is not a choice between using oil derived products and finding a magical solution with LENR. There is excellent research into solar and wind power, for example, research that has made much more progress over the past 25 years than LENR research.

Would I suggest that all research on LENR be stopped? – No, if researchers feel that they still have areas to explore, then fair enough they need to use the evidence they have so far to convince funding bodies to support them. But should we throw lots of funding at an area that is still unclear after almost 25 years, when there are other priorities and research areas providing much better results.

And consider the possibility that LENR does exist, but we do not have the technology to make it work yet. By investing in research in other areas, the technology required to make it work and be useful, might be more likely to arise than funneling huge amount of resources into the one area.

And note I said the “possibility” that it might exist. I would not take this as a given based on existing evidence. One of the exhilarating (and frustrating) things about science is that we are exploring the unknown. Io paraphrase a talk I heard  recently ”science is like hunting for a black cat in a dark room, with the possibility that there is no black cat.”

Of course there is other information confusing the issue – there are websites and youtube videos which purport to describe functional LENR devices. I must admit I’m skeptical of such claims as they come across more as advertising than as science, but if they do in fact work, then why would we need to to invest more time and money into researching LENR? When science/technology makes it to working prototypes this is usually where industry will typically take over.

In the meantime claims of conspiracies, cover ups and insults are inaccurate/have no value.

 

 

 

 

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