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OttomanScribe said:
Hey ScienceGAF, I have a question if I am permitted to ask?

What would explain the variable winters/summers in the world of A Song of Ice and Fire? I was thinking on this the other day and I didn't want to speculate as I am unsure.
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George R R Martin has said in interviews the reason for the seasons is magical in nature and will be revealed before the end of the series. Therefore, there can be no scientific theory that explains it :P
 
Amir0x said:
George R R Martin has said in interviews the reason for the seasons is magical in nature and will be revealed before the end of the series. Therefore, there can be no scientific theory that explains it :P
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Aww... no fun. I was hoping for a 'science of discworld' kind of thing. Oh wells. Thanks for the heads up!
 
Gorgon said:
Perhaps that will be useful, but I'm not sure I'll be working with the bacteria and their interaction with the human host proper. If this PhD goes ahead I'll be working in microbiology proper with pathogenic bacteria. It will be more along the lines of bacteria life-cycles, transmission from animals to humans with groundwaters as the medium between both, environmental microbiology, perhaps epidemics. I'm not sure, but I think I will be doing this more from the perspective of how the bacteria ends up in the human host and not so much what happens when it gets there.


Thing is, I've graduated in geology and my biological background is stronger in ecology, zoology, biogeography, aquatic ecology, macroevolution, paleontology, etc. Most of my microbiological knowledge has to do with ecology of planktonic microorganisms and paleoecology/micropaleontology. So I'm quite ignorant when it comes to working in microbiology at a more medical/veterinary approach with pathogenic bacteria. That's why I'm trying to get an idea of what would be the kind of textbooks I would need for general background and consultation during such research.
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Then I suggest reading this instead.
 
Sirius said:
How has this not been posted yet...

science.jpg


Funnily enough we were nearing the end of our lecture on Cosmic Microwave Background radiation today when our lecturer popped up the CMB spectrum taken from COBE, followed by this comic. It so much more satisfying when seeing it up infront of a physics lecture, people get it.
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I wish I had a teacher that cool. All I got was a old, boring ass physics teacher who was clearly not up to modern times
 
Boozeroony said:
Then I suggest reading this instead.
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I already ordered Brock's Biology of Microorganisms. Do you think this is going to add anything to that one? Seems like same but with a slight different focus.

By the way, what's your academic background and expertize?
 
Gorgon said:
Oh, thanks, I forgot he was the one who started the thread, lol.
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Hehe, indeed.

At first, people were reluctant to donate faecal metarial for me to examine, but now I'm getting bacterial profiles from the same persons more people want to have their poop analyzed.

Now I have more samples I can ever analyze in the time I'm here. Colleagues asking me whether their poop is already screened for bacterial species and whether it is similar to other family members. Once they see the results, the are really enthousiastic.

It is a great ice-breaker too, when starting a conversation. ;)
 
Gorgon said:
Boozeroony, the book you suggested looks a lot like Brock's book. You think I should get both?
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No, get Brock's. Can't go wrong with it.

No need to burn your money on books you only open twice.
 
Boozeroony said:
No, get Brock's. Can't go wrong with it.

No need to burn your money on books you only open twice.
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Thanks. Another question: do you recomend that I get a book on lab technics in microbiology? Also, what books do you think I really should get and find useful?

By the way, if this PhD goes ahead, I'll be making analysis of shit too, except this time it's bird shit lol.

Thanks for everything, man.
 
Gorgon said:
Thanks. Another question: do you recomend that I get a book on lab technics in microbiology? Also, what books do you think I really should get and find useful?

By the way, if this PhD goes ahead, I'll be making analysis of shit too, except this time it's bird shit lol.

Thanks for everything, man.
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This one seems pretty good. I never read it though, so I can't be sure.

Immunology, Bacteriology and possibly a good biological dictionary.

I'd suggest to contact your future employer to check whether they already have books you can read. May save lots of money.

You're welcome, I'm glad to help.
 
Scientists on the Trail of Mystery Molecules

Space scientists working to solve one cosmic mystery at NASA's Ames Research Center, Moffett Field, Calif. now have the capability to better understand unidentified matter in deep space. Using a new facility so sensitive that it can recognize the molecular structure of particles in space, researchers now are able to track unidentified matter seen for the last century absorbing certain wavelengths of light from distant stars.
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http://www.astrobiology.com/news/viewpr.html?pid=33649
 
Need some imput from the microbiology croud here. Are books like Benson's Microbiological Applications
http://www.amazon.com/dp/0077302133/?tag=neogaf0e-20

or Microbiology: A Laboratory Manual

http://www.amazon.com/dp/0321673875/?tag=neogaf0e-20

books that teach the basic lab procedures and technics or are are they made to work only in the classroom with lab exercises? Since I'm not going to have standard classes/courses in microbiology I'm searching for something that actualy gives the instructions on how to do something, like isolating, culturing, that kind of stuff to complement what my coleagues will need to teach me.
 
Gorgon said:
Need some imput from the microbiology croud here. Are books like Benson's Microbiological Applications
http://www.amazon.com/dp/0077302133/?tag=neogaf0e-20

or Microbiology: A Laboratory Manual

http://www.amazon.com/dp/0321673875/?tag=neogaf0e-20

books that teach the basic lab procedures and technics or are are they made to work only in the classroom with lab exercises? Since I'm not going to have standard classes/courses in microbiology I'm searching for something that actualy gives the instructions on how to do something, like isolating, culturing, that kind of stuff to complement what my coleagues will need to teach me.
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Generally speaking, you can read about the basic techniques of microbiology in books like that one and get a gist about what you need to perform them. Basic microbiology, like serial dilutions, plate counting, streaking and spreading etc hasn't really changed in many, many years.

Looking at the preview of the bottom book, it seems decent for that purpose. Not sure about some of the techniques - the one about culture transfer between tubes seems a bit awkward to me, for example, holding two tubes in one hand and using the palm of the other hand (holding the loop) to uncap both of them. It might work in a classroom setting, but in a fast-paced commercial lab, that seems like it'd be awkward to me and thus, may be slow and may increase the chance of a spill. But you may get good at it with practice.

As you probably realize already, no book is a substitute for actual practice - particularly since everything has to be done aseptically. You'll need a fair bit of manual dexterity. Same thing goes for interpreting plates - some plates are easy to read, and others need a fair bit of experience to interpret correctly.

So, I'd say, get one of those books and read up on the theory (especially stuff like calculating concentrations and serial dilutions), and then practice with your colleagues.

Feel free to PM me if you have any questions - I have a few years of experience in food microbiology.
 
The Quiet Man said:
Generally speaking, you can read about the basic techniques of microbiology in books like that one and get a gist about what you need to perform them. Basic microbiology, like serial dilutions, plate counting, streaking and spreading etc hasn't really changed in many, many years.

Looking at the preview of the bottom book, it seems decent for that purpose. Not sure about some of the techniques - the one about culture transfer between tubes seems a bit awkward to me, for example, holding two tubes in one hand and using the palm of the other hand (holding the loop) to uncap both of them. It might work in a classroom setting, but in a fast-paced commercial lab, that seems like it'd be awkward to me and thus, may be slow and may increase the chance of a spill. But you may get good at it with practice.

As you probably realize already, no book is a substitute for actual practice - particularly since everything has to be done aseptically. You'll need a fair bit of manual dexterity. Same thing goes for interpreting plates - some plates are easy to read, and others need a fair bit of experience to interpret correctly.

So, I'd say, get one of those books and read up on the theory (especially stuff like calculating concentrations and serial dilutions), and then practice with your colleagues.

Feel free to PM me if you have any questions - I have a few years of experience in food microbiology.
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Thanks a lot for the imput. I'm just considering getting one of these books because I like to complement the experience you gain by doing with some theoretical background on the "whys" and "hows". That's why I'm asking if these books can be used for that purpose or if they are conceived as some kind of lab exercises that are only useful in actual class teaching.

I'm not sure yet if this PhD is going ahead, I really hope so, but for now its just a possibility. I'll know more in a couple of weeks. If everything goes well and I need to discuss something I'll PM you.

So thanks for everything.
 
Gorgon said:
That's why I'm asking if these books can be used for that purpose or if they are conceived as some kind of lab exercises that are only useful in actual class teaching.
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In general, microbiology lab exercises in class settings are immediately applicable in commercial or research settings because the same basic techniques are used everywhere. So you should find it useful for your purposes - I imagine that you'll have someone else who will fill you in in the more specific techniques not found or not adequately covered in those books.
 
The Quiet Man said:
In general, microbiology lab exercises in class settings are immediately applicable in commercial or research settings because the same basic techniques are used everywhere. So you should find it useful for your purposes - I imagine that you'll have someone else who will fill you in in the more specific techniques not found or not adequately covered in those books.
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I think I didn't express myself correctly, sorry. What I meant was if the books are written and conceived in such a way that they really only work when used in professor-directed lab exercises in a teaching environment. I don't mean that the technics themselves aren't useful outside classes. Like, say, if the various chapters relative to techniques in the books are not really "how tos" but more like bunches of questions and hints, that don't really explain how to do stuff, that is, that are really not complete instructions, and therefore only work in an exercise-based framework for classroom teaching.

Anyway, from your previous answers it seems clear that these books provide descriptions of proceedures and techniques ("how tos"), like in a set of instructions, and that's what I'm searching for.

Thanks for everything.
 
Raist said:
Context? Well huh I dunno, I mean the process itself, what do you think of it?
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I think it's needed and acts as a first screening for inconsistency. It garantees, to a great extent, that all the established protocols are followed and that the research is conducted to acceptable standards and to a certain extent valid in whatever data it produces. Discussion of details and criticism from peers can then follow. It does have it's problems of course, but so does democracy. It may be far from perfect, but it's the best we have.
 
The science community's peer review process is far from perfect, but I was having a conversation with a historian friend of mine the other day, and damn we wish the social sciences had peer review like the natural sciences!
 
OttomanScribe said:
The science community's peer review process is far from perfect, but I was having a conversation with a historian friend of mine the other day, and damn we wish the social sciences had peer review like the natural sciences!
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Well, you guys also have peer-reviewed journals for scientific publishing. The problem is that the nature of the social sciences makes it far more difficult to prove or disprove something than the natural ones and is far more open to speculation.
 
Gorgon said:
Well, you guys also have peer-reviewed journals for scientific publishing. The problem is that the nature of the social sciences makes it far more difficult to prove or disprove something than the natural ones and is far more open to speculation.
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A big part of it is the difficulty of defining what a good journal is. We have some bodies that try to regulate historical journals, but you get some bizarre ones that get A ratings, when they are REALLY not, through loop holes or corruption or whatever :(

The thing about history is that for an educated historian or sociologist, one is still using evidence. It is really the way that that evidence is extrapolated upon that is kind of speculation. However the point of peer review is to ensure that all relevant evidence is taken into account. Even on this forum there have been points where the peer review of fellow Gaffers has pulled up sometimes gaping issues in historical narratives that I have understood from ignorance.

Peer review is an awesome tool, it is unfortunately as fallible as humans are. Doesn't stop it from being of aid though.
 
OttomanScribe said:
A big part of it is the difficulty of defining what a good journal is. We have some bodies that try to regulate historical journals, but you get some bizarre ones that get A ratings, when they are REALLY not, through loop holes or corruption or whatever :(

The thing about history is that for an educated historian or sociologist, one is still using evidence. It is really the way that that evidence is extrapolated upon that is kind of speculation. However the point of peer review is to ensure that all relevant evidence is taken into account. Even on this forum there have been points where the peer review of fellow Gaffers has pulled up sometimes gaping issues in historical narratives that I have understood from ignorance.

Peer review is an awesome tool, it is unfortunately as fallible as humans are. Doesn't stop it from being of aid though.
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Yeah, unfortunately, you guys suffer more with the nature of your science than we do in the natural ones. Still, as you say, it's as good as it gets.
 
When I was a kid, I desperately wanted to be a palaeontologist, but I slowly got pushed to the present, first with archaeology and then with standard history.

However I was reading about my favourite dinosaur (Deinonychus) on the internet today and it brought my previous passion all rushing back. Anyone have any good recommendations for popular science books about the modern conception of dinosaurs?
 
DNA Can Discern Between Two Quantum States

http://www.sciencedaily.com/releases/2011/03/110331104014.htm

Science Daily said:
Do the principles of quantum mechanics apply to biological systems? Until now, says Prof. Ron Naaman of the Institute's Chemical Physics Department (Faculty of Chemistry), both biologists and physicists have considered quantum systems and biological molecules to be like apples and oranges. But research he conducted together with scientists in Germany, which appeared recently in Science, shows that a biological molecule -- DNA -- can discern between quantum states known as spin.

Quantum phenomena, it is generally agreed, take place in extremely tiny systems -- single atoms, for instance, or very small molecules. To investigate them, scientists must usually cool their material down to temperatures approaching absolute zero. Once such a system exceeds a certain size or temperature, its quantum properties collapse, and "every day" classical physics takes over. Naaman: "Biological molecules are quite large, and they work at temperatures that are much warmer than the temperatures at which most quantum physics experiments are conducted. One would expect that the quantum phenomenon of spin, which exists in two opposing states, would be scrambled in these molecules -- and thus irrelevant to their function."

But biological molecules have another property: they are chiral. In other words, they exist in either "left-" or "right-handed" forms that can't be superimposed on one another. Double-stranded DNA molecules are doubly chiral -- both in the arrangement of the individual strands and in the direction of the helices' twist. Naaman knew from previous studies that some chiral molecules can interact in different ways with the two different spins. Together with Prof. Zeev Vager of the Particle Physics and Astrophysics Department, research student Tal Markus, and Prof. Helmut Zacharias and his research team at the University of Münster, Germany, he set out to discover whether DNA might show some spin-selective properties.
The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team's results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. These findings imply that the ability to pick and choose electrons with a particular spin stems from the chiral nature of the DNA molecule, which somehow "sets the preference" for the spin of electrons moving through it.

In fact, says Naaman, DNA turns out to be a superb "spin filter," and the team's findings could have relevance for both biomedical research and the field of spintronics. If further studies, for instance, bear out the finding that DNA only sustains damage from spins pointing in one direction, then exposure might be reduced and medical devices designed accordingly. On the other hand, DNA and other biological molecules could become a central feature of new types of spintronic devices, which will work on particle spin rather than electric charge, as they do today.
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quantum mechanics are so awesome
 
Quantum Physics First: Physicists Measure Without Distorting

http://www.sciencedaily.com/releases/2011/06/110602143159.htm

here's an explanation of the double slit experiment they mention: http://www.youtube.com/watch?v=DfPeprQ7oGc

don't let its cheap presentation put you off. it explains the concept very simply and you should watch it before reading the article below if you don't already know the principals of the double slit experiment. jump to about 3:25 for the part specifically about observation.

Science Daily said:
Quantum mechanics is famous for saying that a tree falling in a forest when there's no one there doesn't make a sound. Quantum mechanics also says that if anyone is listening, it interferes with and changes the tree. And so the famous paradox: how can we know reality if we cannot measure it without distorting it?

An international team of researchers, led by University of Toronto physicist Aephraim Steinberg of the Centre for Quantum Information and Quantum Control, has found a way to do just that by applying a modern measurement technique to the historic two-slit interferometer experiment in which a beam of light shone through two slits results in an interference pattern on a screen behind.

That famous experiment, and the 1927 Neils Bohr and Albert Einstein debates, seemed to establish that you could not watch a particle go through one of two slits without destroying the interference effect: you had to choose which phenomenon to look for.

"Quantum measurement has been the philosophical elephant in the room of quantum mechanics for the past century," says Steinberg, who is lead author of Observing the Average Trajectories of Single Photons in a Two-Slit Interferometer, to be published in Science on June 2. "However, in the past 10 to 15 years, technology has reached the point where detailed experiments on individual quantum systems really can be done, with potential applications such as quantum cryptography and computation."

With this new experiment, the researchers have succeeded for the first time in experimentally reconstructing full trajectories which provide a description of how light particles move through the two slits and form an interference pattern. Their technique builds on a new theory of weak measurement that was developed by Yakir Aharonov's group at Tel Aviv University. Howard Wiseman of Griffith University proposed that it might be possible to measure the direction a photon (particle of light) was moving, conditioned upon where the photon is found. By combining information about the photon's direction at many different points, one could construct its entire flow pattern ie. the trajectories it takes to a screen.

"In our experiment, a new single-photon source developed at the National Institute for Standards and Technology in Colorado was used to send photons one by one into an interferometer constructed at Toronto. We then used a quartz calcite, which has an effect on light that depends on the direction the light is propagating, to measure the direction as a function of position. Our measured trajectories are consistent, as Wiseman had predicted, with the realistic but unconventional interpretation of quantum mechanics of such influential thinkers as David Bohm and Louis de Broglie," said Steinberg.

The original double-slit experiment played a central role in the early development of quantum mechanics, leading directly to Bohr's formulation of the principle of complementarity. Complementarity states that observing particle-like or wave-like behaviour in the double-slit experiment depends on the type of measurement made: the system cannot behave as both a particle and wave simultaneously. Steinberg's recent experiment suggests this doesn't have to be the case: the system can behave as both.

"By applying a modern measurement technique to the historic double-slit experiment, we were able to observe the average particle trajectories undergoing wave-like interference, which is the first observation of its kind. This result should contribute to the ongoing debate over the various interpretations of quantum theory," said Steinberg. "It shows that long-neglected questions about the different types of measurement possible in quantum mechanics can finally be addressed in the lab, and weak measurements such as the sort we use in this work may prove crucial in studying all sorts of new phenomena.

"But mostly, we are all just thrilled to be able to see, in some sense, what a photon does as it goes through an interferometer, something all of our textbooks and professors had always told us was impossible."

Research partners include the University of Toronto's Centre for Quantum Information and Quantum Control, Department of Physics and Institute for Optical Sciences, the National Institute of Standards and Technology in Boulder, Colorado, the Institute for Quantum Computing at the University of Waterloo, Griffith University, Australia, and the Laboratoire Charles Fabry in Orsay, France. Research was funded by the Natural Sciences and Engineering Research Council of Canada, the Canadian Institute for Advanced Research, and Quantum Works.
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sorry to post twice in a row, but this is too awesome not to add to this thread.

some really huge strides happening in quantum research. i think the field is going to explode in a few years.
 
Scrow said:
Quantum Physics First: Physicists Measure Without Distorting

http://www.sciencedaily.com/releases/2011/06/110602143159.htm

here's an explanation of the double slit experiment they mention: http://www.youtube.com/watch?v=DfPeprQ7oGc

don't let its cheap presentation put you off. it explains the concept very simply and you should watch it before reading the article below if you don't already know the principals of the double slit experiment. jump to about 3:25 for the part specifically about observation.

sorry to post twice in a row, but this is too awesome not to add to this thread.

some really huge strides happening in quantum research. i think the field is going to explode in a few years.
Click to expand...

Interesting. Will wait for comments after publishing.
 
Wired Science said:
Oceanographers say that more is known about the surface of Mars than the deep seafloor of Earth. They’re right: Only a fraction of our seafloors have been studied. But with oceans covering 70 percent of Earth’s surface, a fraction is still quite a lot.
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I can understand why, yet this is still so mind-boggling. We think we have the Earth all figured out when there's so much we may never know.
 
Sirius said:
I can understand why, yet this is still so mind-boggling. We think we have the Earth all figured out when there's so much we may never know.
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Well, they're "hyperboling" a bit there. Obviously we can "see" a lot more of Mars because we don't have an ocean on top of it. And we have some very nice highrez mapping of it's surface from sattelites. The ocean depths, on the other hand, can't be seen directly for great extentions due to the darkness, but the mapping is good too, and better yet, we have been dragging and sampling the bottoms for a long time (although in a localyzed way), as well as drilling it, something that we are no close to do in Mars to the same extent. So we know different things from different perspectives about both.
 
Anyone knows of a general microbiology forum, where people can ask questions about technics, discuss research, etc?
 
Listened to a radio show about the implications of neuroscience on law. It was a philosophical discussion about some of the long term effects of things like complex tests to tell if someone is lying and other such things. Fascinating.
 
What a great thread!

I should introduce mahself. I graduated in Cell and Molecular Biology two and a half years ago, and went straight into a PhD in Molecular Medicine. I work in neuropsychiatric genetics, performing a functional follow-up of a gene implicated in autism via a genome wide association study. Everything in our group is exome sequencing this and next-gen sequencing that, so I feel lucky as a functional genomics biologist there is a lot of work up and coming for people will such skills (as it's not enough to just implicate mutations in disease, we need to know the function!). My work is mostly just research as part of a consortia, but there are people in my group who meet with patients and take DNA samples from them, so hopefully one day those people or their relatives will see treatments come about due to their participation in genetic studies.

I think the most interesting thing I have learnt recently was at the most recent European Society for Human Genetics meeting. There was a seminar about intellectual disability where they were discussing how, using next-gen sequencing, many of the mutations that they have found to be risk factors (or even causative) were not in 'neuron specific' genes, but in general 'housekeeping genes', cell adhesion molecules etc. This was interesting for me in terms of my research, but I also think it demonstrates the power that next generation sequencing technology has in enabling us to find genes implicated in a disorder that people had ignored for one reason or another. It goes to show you that the 'hypothesis free' approach of genome wide association studies and whole genome sequencing isn't all bad. ^^


OttomanScribe said:
Listened to a radio show about the implications of neuroscience on law. It was a philosophical discussion about some of the long term effects of things like complex tests to tell if someone is lying and other such things. Fascinating.
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Were they discussing fMRI? Some of the clinical psychologists in my group use that with patients, I've seen some of their raw data at their presentations, they really are fascinating to look at - like a heat map of brain activity in 3D. Mammalian brains are just so cool!
 
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