Wednesday, 19 December 2007
Question: If the hearty nature of a sneeze is meant to release any irritants that have built up in our respiratory system, why is is that some people sneeze gently or internally or make squeaky sounds when they sneeze. How does a person who sneezes in this way release anything within their respiratory system.
PS: I have considered the actions of coughing and the mechanical actions of cilia but how could these possibly create the outcomes of a violent sneeze.
Tuesday, 9 October 2007
Saturday, 18 August 2007
There are several factors which contribute to aging in modern society: mainly genetics, diet, stress and lifestyle factors. I have often wondered whether sugar does really cause aging most especially when i develop sugar cravings usually satiated by chocolate and my newly found craze of Nando's chocolate mousse. However I have never actually looked at these studies which support the findings that sugar induces premature aging but mainly just believed the hype in the media. So, I decided to briefly review a recent manuscript which asks this question and conducts experiments at the molecular level, and confirms previous findings. So as i speak, i believe i am spiralling into premature death by chocolate.
A manuscript by Berge et al. (2007) demonstrated that normal human epidermal keratinocytes (primary cells) treated with 100 mM glucose or 0.1 mM gyoxal* for three days induced premature aging. Their experimental methods included examining the phenotype of cells, cell proliferation and cell viability assays, an assay to examine glycoxidatively damaged proteins, and examination of differentiation markers of the cell.
Findings: Using cell proliferation and cell viability assays, the cell number, proliferation rate and viability was measured and found to have decreased in a dose-dependent manner at a glucose concentration of 100 mM and above relative to controls. In contrast, 0.1 mM of glyoxal and above induced a reduction in the previously mentioned parameters in a dose-dependent manner relative to controls. The LD50 for glucose and glyoxal was 200 mM and 50 uM, respectively. The authors state that the possible reason for the difference in LD50 values could be due to glyoxal having a higher reactivity and easier penetration of the cell membrane. Examination of cell morphology demonstrated that cells treated with the same levels of sugar induced vacuolation (formation of vacuoles) and increase in cell size, both of which are characteristic of senescent** cells. Results from assays targeted to measuring aging cells, including the senescence-associated beta-galactosidase and protein glycoxidation***, were significantly higher in cells treated with the sugars compared to control cells after three days of treatment. Glucose caused a 52% and 58% increase and glyoxal a 44% and 68% increase in the senescence-associated beta-galactosidase and protein glycoxidation assays, respectively. Glycoxidation of proteins targets these proteins to be degraded by the proteasome because they are of no use or unwanted by the cell. Proteasomal degradation is one of a few ways in which unwanted proteins are targeted and removed by our cells. As a measure of unwanted protein removal, the group measured proteasomal activity and found that glucose-treated cells had an 11% increase in proteasomal activity. Glyoxal treated cells had a 3% decrease which the authors state as "unchanged". Differentiation was examined using involucrin level measurement against a differentiation agent, calcium. Using a positive control of 1.2 mM calcium, glucose treatment of cells resulted in involucrin levels lower than the positive control whereas glyoxal treatment resulted in involucrin levels similar to and higher than the positive control.
Conclusions: Glucose concentrations of 100 mM and glyoxal concentrations of 0.1 mM and the above indicators of cell senescence in human epidermal keratinocytes have re-confirmed that sugar is able to induce premature aging.
That Mars bar doesn't look so appetising now, does it?
Source: Berge, U, Behrens, J and Rattan, SI. Sugar-Induced Premature Aging and Altered Differentiation in Human Epidermal Keratinocytes. Annals of New York Academy of Science. Volume 1100: 524-529 (2007).
* The paper refers to the term glyoxal, which i assume is methylglyoxal. Methylglyoxal is a by-product of glycolysis (sugar breakdown).
** Cellular senescence, which is when cells arrest in a non-dividing state, is synonomous with aging in the biological context.
***Glycoxidation is the oxidative alteration of a protein by a sugar and forms advanced glycation end products which are known contributors of aging.
Australia has been celebrating science for the past ten years by running National Science Week (NSW) annually. Today marks the first day of the 10th NSW (18th-26th August). Various science related events will be held throughout the country showing-casing and celebrating science and raising awareness about the importance of science.
Happy NSW everyone!
Wednesday, 8 August 2007
Monday, 6 August 2007
The Australian synchrotron funded and run by tax payers, opened its doors for the first time last week in Clayton, Victoria. The massive facility which is about the size of a football field cost just over $200,000,000 and almost six years to construct from the time it was proposed to the opening day (31st July 2007). Currently running 24 hours a day for six days a week, the synchrotron is thought to be able to produce synchrotron light a millions times brighter than the sun! Synchrotron light can be used for various applications in biology (eg. protein crystallography), material sciences and physics. The facility which is encased in concrete walls is made up of two circles. The inner circle, named the booster ring is responsible for accelerating electrons very close to the speed of light which are initially fired off by an electron gun. The electrons are then collected by the outer storage ring. There are several catchment areas which come off the circular rings which will eventually represent nine labs. Of the many synchrotrons located around the world, having a local facility will be highly beneficial towards the progress of science in Australia by cutting down travel costs, experimental time and transport problems associated with carrying out experiments overseas.
ABC Radio National (The Science Show, 28th July 2007)
Wednesday, 1 August 2007
In my readings over the past few weeks I have encountered a few articles directed at scientists describing the complacent attitude of reporting science stories to the media. This may be due to inefficient or misinformed reporting on the part of the scientist or the media, which would be unknown to the reader. An article I read today in “NewScientist” titled “Not all that it seems” (28th July 2007) highlighted this problem once again, describing a story where a reputable newspaper described the discovery of a new gene to be the cause of restless leg syndrome (apparently the actual existence of this conditions is disputed, which is news to me). This reporting was incorrect on the journalist’s part. Anyway, the point being is that the newspaper article was misinforming the public. Another example, closer to home, occurred when a colleague of mine recently identified a new mutation thought to be responsible for a disease which was quite significant to her field of research. The state and several local newspapers published this story with each article being reported differently but accurately. The main gist of one article in particular was correct but there was a line which read something similar to this: “The gene was responsible for attacking a part of the protein”. This statement was incorrect and could never be correct for any matter. First of all, genes don’t attack proteins and secondly, the gene is what encodes the protein ie. the gene is the precursor of the protein. I’m not sure what happened to the lines of communication between the scientist and the journalist in this case. This may be an obvious question but shouldn’t the scientist have read the final result before it had been submitted for publication? A couple of days ago, I read another article in “The Scientist” (“Special feature: How should scientists sell science?”) addressing this issue and even setting up an online survey to get a scientist’s perspective. The article ended with this statement.
“With your help we can gauge how the life science community and people who have an interest in life sciences feel about the issue of framing science, and add to the growing debate that could help shape the future of science communication in the media”. ("The Scientist")
There seems to be a missing link between information being passed on from the scientist to the media. To bridge the gap, a scientist not only needs to be able to relay the important messages to his or her colleagues but also the general community at a suitable level that is also truthful. It’s is highly important to keep the public informed on scientific findings; after all, research is publicly funded in a lot of cases and progress in fields of disease research for example is highly encouraging to hear about. In addition, addressing the public on a lay level gives the scientist a different level of understanding and reminds them of the "big picture" which is often forgotten or overlooked because of the specific nature of research.
Unfortunately, this mis-reporting has been on-going for too long now. Fortunately, a new breed of journalists are emerging: there is an increase in jounalists who are also researchers or have expertise in the medical field. In addition, i recently discovered that not only is my own university offering science communication as an elective in a science degree but there is a science communication degree which encompases both journalism and basic science.
PS: A few weeks after writing this post, I had the opportunity to talk to a media consultant of a large medical research institute. One of my questions to her was regarding the misinformation of science in the media and how it could be avoided. She replied by giving me the one reason as to why this occurred: The time delay which occurred for the media to write an article and subsequently get it proof-read by the scientist was too time consuming. If this practice was to occur it would be impractical given the competition between media organisations to report breaking news. She also said that this practice could not be avoided and it was the responsibility of both the scientist and journalist to relay and exchange information as accurately as possible during the interview.
NewScientist, 28th July 2007, page 5
The Scientist, 30th July 2007
Saturday, 28 July 2007
A recent article in “The Scientist” described architects using and adapting from biological systems to design buildings (“Designing buildings, using biology”, 27th July 2007). I thought it was an interesting and sensible new-age concept because it does make sense to create an unnatural object that will be subjected to nature by mimicking nature itself. Although most architecture has stood the test of time, it is not always aesthetically pleasing and does not take advantage of what nature has to offer. For example, the article states that one of these modern architectural firms “ensures that each house gets the most exposure to light and works around the natural movement of groundwater. Like in a living organism, each part of this project is influenced by its relationship to the other parts”.
Below are just some points from the “The Scientist” article which I thought were pertinent to what I will introduce next.
“Before the 20th century, most architects detached their work from the place it was designed to go. Rather than understanding the city as a living, dynamic organization, these earlier architects established static forms and rules that did not take the environment into account. That's why the skylines of so many cities contain a series of boxes that often don't relate to each other, and could essentially be picked up and stapled down anywhere else.”
Otto (who you could possibly call the protagonist of the article) “recognized that natural systems are self-stabilizing, optimization machines. Any changes in the internal or external environment have a direct consequence on the form, so why not design the final form by imitating the processes that create the form of natural objects?”
“Today, more designers are accepting the idea that physical structures are a part of a larger organic network, and that the structure, forms, and environment influence each other, just as in living systems.”
I find the last concept (quoted above) really interesting and is closely related to James Lovelock’s Gaia hypothesis, which I heard about for the first time a few weeks ago after listening to a radio interview.
“The Gaia hypothesis is an ecological hypothesis that proposes that living and nonliving parts of the earth are viewed as a complex interacting system that can be thought of as a single organism". (Wikipedia)
Lovelock (in collaboration with Lynn Margulis) introduced the term “gaia” to describe a number of concepts for earth but basically describing planet earth as a single, evolving, self-regulating, physiological system at at state favourable for its inhabitants (living and non-living). Lovelock was “concerned with the working of a whole system, not with the separated parts of a planet divided arbitrarily into the biosphere, atmosphere, lithosphere and hydrosphere”. He states that “conventional wisdom sees earth as a dead planet made up of inanimate rocks, oceans, atmosphere and inhabited by life”.
When Lovelock initially proposed the gaia hypothesis in 1971, it was criticised by scientists because it couldn’t be proven scientifically and as the earth was a system incapable of reproduction, it was not considered to be alive and therefore the hypothesis was scientifically unsound. Lovelock uses earth and the human body as an analogy to make his argument. If earth was compared to the human body, for example, the rivers and oceans as the body’s cardiovascular system or the forests as the body’s respiratory system, then each system is unable to exist independently. All systems work together and exist in harmony. After recently reading one of Lovelock’s books (“Gaia – medicine for an ailing planet”), I will acknowledge some of his ideas and will adopt this new philosophy to view different systems that I am not familiar with, such as our planet. As a scientist in the making, I don’t agree that all things have to be scientifically proven to be real or truthful (cue shifty look) but I am open to new ideas and would like believe that this idea of gaia is plausible.
Now to a less relevant point, the main notions of this book revolve around the gaia hypothesis and the argument and examples of how humans have inflicted a “disease” on the planet. Initially though, when introducing the gaia concept, Lovelock describes the problems with today’s “reductionist” scientific approach and believes that it is not the best approach to study global changes (I can understand the latter point and agree that it would be a hard task to accomplish). He states that today’s science is not pragmatic, does not consider the systems wholly and therefore takes too long to make progress however he does not think the “scientific method” should be abandoned. While I agree with this to some point, I think some systems (whether ecological, biological or medical) have to be dismantled to be studied in detail or microscopically. This approach, although time-consuming, may not always give immediate answers but the outcomes are still valuable and have been responsible for some of great scientific discoveries in history. Further into the book , Lovelock goes on to say “Not all things reductionist are bad, nor are all things holistic good. The reductionist, bottom-up view can be needed just as much as the holistic. One of the great rewards of science is that sudden flash of understanding that comes when holism and reduction meet”. Now that’s what I like to hear.
Gaia - medicine for an ailing planet (James Lovelock, 2005)
Saturday, 14 July 2007
Today I had an experience which has finally resulted in me rejecting the Hindu's concept of karma. The idea of rejection had been looming within me for the past few months but i did not know of any other way to explain it. Today, I discovered another concept which i believe is more plausible but currently know very little about. I have to explain the full story to make my point. I was walking down a street in the city today when I noticed a homeless man coming my way. He had stopped all the people who had passed him, asking them for money, and he did the same to me. I have always thought to myself that if a homeless person ever asked me for money then I would tell them that I would be happy to buy them food rather than give them money directly. Anyway, this did not come to my mind at the time and I immediately refused this man's request and then felt a bit silly for not carrying out my premeditated idea. A short time later, I was waiting outside a shop and I had a view of this man in the rear-view mirror of my car. The idea of offering this man some food was heavily playing on my mind. After a bit of hesitation I walked up to him and told him that I would be happy to buy him some food but refused to give him money (he asked me for money for the second time and when i asked him what it was for, he said it was for food). Anyway, he accepted my offer and I bought him some food, for which he was very grateful. Later today I was walking through a hospital when I saw a $10 note on the floor. I looked around to see whether anyone had dropped it but there was no one in close proximity so I picked it up and decided to keep it. So that's my story. Some people may call this karma (i.e. you reap what you sow, where the effects may be immediate or delayed). Normally I would have put it down as karma as well, but for the past few months I have been questioning the concept of "karma created by God" because that is what I have believed for some time now. For a long time I had simply accepted that karma was managed by God without questioning it because it is a strong belief in Hinduism, which I am nominally and have been practising perfunctorily. I am also a believer of "signs" and "things happening for a reason" because some experiences I have had are too kooky to be coincidental, and in the past I have believed that these were also a result of God's intervention. However over the last few months I have questioned this belief which has eventuated to me renouncing my belief in karma and other concepts that are managed by God. I may later revoke what I am about to write but right now I feel this way. I had thought that if I were to renounce the concept of "karma", "coincidences" and "things happening for a reason" through God, I didn't know of any other way to explain these incidences because I don't believe in coincidences for everything. However just today, I happened to stumble across the works of Carl Jung. Before I go any further I will admit that all my readings on Carl Jung and his theory of synchronicity, which was done only tonight, have been from Wikipedia and other internet sources, so I am not fully informed on his works. Also, I don't know how credible some internet sources are so I may be misinformed and may well sound it. Jung was a psychologist who formulated the term "Synchronicity". The standard definition of snychronicity according to Wikipedia is "the experience of two or more events which occur in a meaningful manner, but which are causally inexplicable to the person or persons experiencing them". However in Jung's definition, "the events would also have to suggest some underlying pattern in order to satisfy the definition of synchronicity". Jung believed that "many experiences perceived as coincidences were not merely due to chance but, instead, suggested the manifestation of parallel events or circumstances reflecting this governing dynamic". (Wikipedia)
Another website had this explanation:
"Synchronicities are people, places or events that your soul attracts into your life to help you evolve to higher consciousness or to place emphasis on something going on in your life. The more 'consciously aware' you become of how your soul manifests, the higher your frequency becomes and the faster you manifest positively. Each day your life encounters meaningful coincidences, synchronicities, that you have attracted, on other words created in the grid of your experiences in the physical".
Now all of the above sounds synonymous to karma in a way but not the Hindu belief of karma, where karma is given out by God. I don't think Jung attributed synchronicity to the supernatural which is why I think it is a perfect reasoning for SOME incidences. This may also sound like I am renouncing my belief in God and truthfully I have lately been thinking about God's existence more seriously than I ever have before. However, right now, I am renouncing the "God managing karma and other coincidences" concept which I have described above; and will happily accept synchronicity over karma. The reason why I have used capital letters for the word "some" is because I don't think you can put everything down to synchronicity as some experiences occur just by plain coincidence. Also, Hindus strongly believe that the effects of karma are carried over from past lives and continued on when the soul is reincarnated. I believe that it is unhealthy to assume that suffering in your current life could be a result of your doings from your previous life, even though I am sitting on the fence for the notion of reincarnation. At this present time, i am happy to believe that everything that has occurred in this life is manifested ourselves from this current life. I will conclude this post with a quote from the Dalai Lama, which has resonated with me: "I am open to the guidance of synchronicity, and do not let expectations hinder my path".
Thursday, 5 July 2007
Wednesday, 4 July 2007
So now everyone is jumping on the green bandwagon and looking to become more environmentally friendly and this includes science laboratories. From my observation, the ‘modern-day’ green movement began to escalate quickly after “An inconvenient truth” was released. I think this movie/documentary (which I still haven’t seen) opened the eyes of a large portion of society who were unaware of global warming (including myself) or who had turned a blind eye to it. As far as I am aware, "Nature" (which I don’t have the privilege of reading online) and "The Scientist" are just a couple of science journals that have recently published articles about making the lab more environmentally friendly. However, long before Al Gore, Nature or The Scientist, one of my ex-co-workers actually raised the question of how much scientists contribute to the destruction of the environment. I’m uncertain about labs in other disciplines (eg. engineering, agriculture) but if you’ve ever worked in medical science lab, you would know how environmentally un-friendly they were. Starting at the lab bench: My work is at the molecular level therefore liquid handling is in microlitres and millilitres and one of the most highly utilised apparatus for this level of liquid dispensing is the hand pipette which requires disposable plastic tips. Most of my work requires the use of a very large number of these plastic tips for dispensing biological materials, solutions or enzymes. For each sample, a new tip is required for each ingredient. Then there are hand gloves which are used to protect the scientist from biological or chemical contamination and also to protect the sample from human contaminants. Tissues, Eppendorfs (small tubes for holding small quantities of volume), regular tubes, etc, etc. All of the above mentioned must then be incinerated because it can contain hazardous human cells, pathogens or genetically modified organisms. The process of waste incineration consequently produces gas emissions (including carbon dioxide). In addition to these plastics, many products are usually enclosed in their own plastic casing or packaging because our experiments require the products to be sterile upon use. A large quantity of paper and plastic waste is accumulated just alone from the packaging of products.
Scattered around the lab are commonly used equipment/apparatus which require large amounts of electricity to run: water baths, incubators, rockers, mixers, balances, a radio (if in my lab), fume hoods, ultra-cold freezers, etc. Most of these equipment are left turned on or on standby due to the inconvenience of start up times when needed to be used; and also because they may be incubating biological specimens.
An important point mentioned in "The Scientist" article (Can labs go green?, volume 21, page 6) was that a lot labs did not have windows and therefore relied upon artificial light sources. Medical research facilities usually comprise of several labs which are fitted with standard fluorescent lights. Unfortunately, most of the time, the lights in a room will be left on even after one use and a single room can contain several light fittings. I’m not sure why many labs were designed without windows and still continue to be designed without windows. Maybe to avoid distraction from the outside or maybe to use space economically or maybe to protect biological specimens from the UV light emitted from sun.
The above are just a couple of my observations of energy usage in the lab and I’m sure there are many points I have missed. Prior to writing this post, i was unware of the real impact that running a lab had on the environment compared to a household or a building but according to the sources cited by The Scientist, it is significantly greater. Significant enough to initiate projects such a Labs21 ("a voluntary partnership programme dedicated to improving the environmental performance of US laboratories" - Labs21). It will be interesting to see how far the lab will evolve in an effort to sustain the environment.
In conclusion i would like to ask this question: Does the benefit of medical research out-weigh its negative impact on the environment or vice-versa? On one hand, medical scientists are trying to better the quality of life for humanity but on the other hand we are using vast amounts of energy to produce, use and dispose of products and equipment, all of which is contributing to the detriment of the environment and humanity. I know that when I’m working in the lab I am doing my bit for the environment and my ex-co-worker will definitely back me up here.
The Scientress remains elegantly poised as she waits patiently for a signal from the agarose gel. As she hovers, the intensity of her eyes pierce the wells of the gel which give in submissively, allowing her to begin loading the DNA into the wells. Her chemical-infused white plumage and dishevelled mane fall victim to the beads of sweat trickling from her forehead and down her spine. The air is thick with concentration. Her alert senses make her aware of the incessant electric hum of distant power packs in the wilderness, running DNA in the race for results. However, her strong dedication to the gel makes her unaware of territorial scientists lurking between lab benches in the background trying to distract her from her efforts to submit within three years. The laboratory is her savannah.
Saturday, 30 June 2007
Sunday, 24 June 2007
Today (June 1st) marks the first year anniversary of starting my PhD (ie. the start of my second year). I dont know whether i should be happy or sad. I guess i feel a little of both:
- I've made it through my first year
- I dont have the urge to throw it all in
- I actually have results which i will present at a conference next week.
- That's one year gone and now i have even less time to complete what feels like would take 5 years to finish
- I can't walk around and blame all my mistakes on being a first year student- I actually have to sound knowledgeable now as opposed to acting it
Anyway, regardless of how i felt, i stopped by my favourtie pastry shop this morning (hey, i was in the neighbourhood, sort of) and picked up an almond flan to share with my colleagues. They all looked at me a little confused but nevertheless, wished me well.
I am feeling ecstatic right now (in the scientific sense). Ater spending a morning in the lab (yes, another Saturday), i have manged to produce one of the best results yet. Last weekend, i showed an interaction of my two proteins in the mammalian system using one method and this week i showed the same interaction in the same system but using a reciprocal method. This result can also be used for my work and strengthens our working hypothesis that one protein is involved in the cell signalling events of the other protein. Although i have to repeat this experiment because i accidently broke the gel in the most important spot, i am more confident that i can get the same result if replicated.
Ahhhh...A big sigh of relief from my part of the world. I had a very satisfying day in the lab today (yes, a Saturday). I finally got the result i was looking for and a result that takes me one step closer to fulfilling one of my goals for 2007 ie. to present my work at a conference. With a little tweaking of my experimental protocol i was able to show the interaction of two proteins that i am studying. I had been trying to do this for the last 5 months (in two different systems - in vivo and in vitro) and i was able to show an interaction on two separate occassions but the interactons were very weak. Today's result gave me a strong indication of binding. Yay! Thank you phosphatase inhibitors.