http://www.theguardian.com/science/2013/dec/09/nobel-winner-boycott-science-journals
http://www.theguardian.com/science/2013/dec/09/nobel-winner-boycott-science-journals
Now who would have thought of that..Nobel laureates stand up against major-publishing group bullying!
Seth Raphaels shot on the Randi Foundation 1 Million dollar
Seth Raphaels shot on the Randi Foundation 1 Million dollar
Seth Raphael claims to be a computer psychic, or that his computer is psychic, or a psychic. I got confused half way trough. But watch this and prepare to get blown of your chair!
Microscopy four – Focal length
Last time we ended scratching the topic of focal length, and I told you that this is going to be complicated. Don’t worry it will be. Yet, focal length in itself is rather easy and straightforward to determine and also to explain, if you’re not going into details. It is a characteristic of the lense you’re using. So just imagine having a magnifying glass and you use it to focus sunlight, as if you would try to use it for starting a fire. If you take all the light the lense is capturing and focus it on a single spot on the other side, the distance between the lense and the point that lightspot is most concentrated, that is the focal length or focal distance. It is a physical property of the lense, based on the lenses curvature.
On a berfectly biconvex lens the focal distance would be equal on both sides of the lense. In the context of microscopy we will assume it is that way to make things easier.
Theoretically spoken, and inlcuding some equations, one could express that as following
1/S1 + 1/S2 =1/f
with f being the focal distance and S1 being the distance between object and lens and S2 being the distance between lens and eye/image.
Assuming we are producing a real image here, and with both distances being the same, the image produced would be exactly the same size as the object observed.
The magnification comes into play as following.
M= – (S2 / S1) = f / (f – S1)
That sounds complicated, but what it really tells is,if M is bigger than 1, the image will be magniefied, if it is smaller, than it will be shrinked down. Which is exactly what is happening within a binocular, basically.
What happens in a microscope is turning the image upside down for a real image, which you would not see though as it would be same size as your microscopically small object. But, of course light rays don’t just stop there, so on the far side of the focal distance, on our side of the lens, the image is crossed again and the lightrays spread out, creating a virtual image that is upright again, and magnified, using another lens in the eyepiece to sharpen and focus it again back onto our eyes. and to the image we see.
See the image below to get a better idea of that, if your brain works as visual as mine.
Microscopy Three – Microscopic vs. Macroscopy
An ant as imaged using a scanning electron microscope (SEM) (Photo credit: Wikipedia)
English: A big surprise in the woods at Crich Tramway Village A new attraction at Crich Tramway Village is the Woodland Walk & Sculpture Trail. Near the Wakebridge end of the trail is this giant wood ant. You probably wouldn’t want to come across this as dusk approaches! (Photo credit: Wikipedia)
And here we are with part three on microscopy; what microscopic and macroscopic means.
Let’s have a look at that, and start right at the beginning. If you think about scientific terms, it’s always, and I mean always, a good idea to look into the ethymology of the term and/or thing you want to know more about. In this case, we are talking about micro and macro. Mikros is a greak word (for once not a latin one, but scientists tend to switch between those two languages a lot), that means small. Makros on the other hand descirbes something big. Now this sounds very simplistic and not at all like something, that could be used as a definition; in the end a mouse is small too, but you wouldn’t need a microscope to see one. However, in a still simplistic view, the microcosm, that you would observe with a microscope, is that part of our world, that you wouldn’t be able to see without one. As opposed to the macrocosm, which you can. Thinking of that things start to come together a bit more. But I, myself, am still not quite satisfied with that definition either. What other properties could there be to nail it down a bit more proper.
In order to do so, we shall investigate three items, and their properties, a bit more closely; a binocular, a microscope and a magnifying glass.
A microscope will make something small, and close, within a narrow focus plane appear larger then it acutally is. A binocular on the other hand, will make something far away, typically bigger, almost without concerning about a foual plane (the focal plane at some point is basically infinite) appear smaller then it actually is. We only rearrange that image in our brain back to it’s expected size. And finally the magnifying glass would basically do both things, but it would turn blurry or upside down. How is this possible?
The answer lies within what is called focal length/width (and a subsequent arrangement of more lenses for further adjustment)
Now this is a very much complex topic, and I will leave you with this little teaser until my next post, where I’ll explain focal distance.
Microscopy Two – History of the lens
Philately, Magnifying glass shows the magnified image of the Deutsche Post 1 Reichsmark postage stamp issued on May 12 1946. Français : Étude à la loupe d’un timbre de la poste allemande de 1 Reichsmark datant du 12 mai 1946. Philatélie, loupe. (Photo credit: Wikipedia)
So here’s another short one for the microscopy series. The “what was before” the microscope part of it, if you want to phrase it that way.
The central part of a microscope is the lens. But a lens is also a plant (Lens culinaris) and the name of it’s very own fruit, called Lentia in latin. So how do these two connect, you might ask. And that is really straight forward. In the 1st century AD the romans started experimenting with various shapes of glass, not only to put them in windows but also convert them into beautiful pieces of artwork and jewlery for example. One of the shapes the cam up with resembled that of a lens, a common edible at that time. So it was roundish, flat at the edges and growing in thickness towards the center with a rather regular curvature. When those romans looked through that see-through, lens shaped obejct they discouvered that objects on the far side of it will appear bigger, and that was the very moment in history the magnifying glass, or lens, was born.
Without a lens, no microscope, no telescope, no binocular, in fact not even normal glasses would work. So I guess once again we have to be thankful for those great inventions that date back over centuries, without which our society would just not quite work as it does.
So now that you know where the lens comes from, my next post will focus a bit more on some of the other things I just mentioned. Namely binoculars, telescopes, magnifying glasses, regular glasses and what seperates them from what we consider a microscope.
Microscopy One – Introduction
English: binocular microscope Français : Loupe binoculaire (Photo credit: Wikipedia)
I’m so sorry for not blogging for so long, that will change now, since I am going to try summing up microscopy. Not quite an easy topic, but since I’m dealing with microscopes nearly every day, and teaching every once in a while, and I found that people using microscopes often know too little about how they work and where they come from. So the next couple of posts will focus on just that, history and principles of microscopy. Enjoy and cheers
Scientists declare bio-nuclear war on cancer!
Listeria monocytogenes (Photo credit: AJC1)
Anyone seen “I am legend”?
Well I did, and I very well remember the intro sequence (which is great by the way).
Ahhh, WTH, just take some two minutes and have a look at it, it will take you to the point of departure of what I’m going to talk about in the next couple of lines.
Done? Good. So lets talk about that. wouldn’t that be totally awesome? Having some tiny agent that would eradicate all those nasty cancer cells? Of course, we all know that in the movie this cure goes terribly wrong and mutates people into mean, killing zombies. Yeah, ain’t nobody got time for that, right? But hey, if you peek over to Star Trek you see all those cool things that have been invented for movies and were then turned into actual science and maybe even products, just think of the cell phone and the communicator, and vice versa.
Alright so we’ve seen the fictional side of it, lets have a look on the actual science part.
Because, if you think the movie idea is cool, then be prepared to be blown away. A group of scientist in New York just officially declared a bio-nuclear war on cancer. The group of amazing people around Wilber Quispe-Tintaya and Claudia Gravekamp modified a strain of Listeria monocytogenes, a human pathogen often found on food, that is usually succesfully suppressed by the immune system of healthy people, but can tackle you down too the loo for quite some time. If the immune system is weakened though, it can cause some more severe symptoms. And there is kind of the beauty of it actually. Because, in cancer cells that is what happens, the immune system is suppressed, otherwise the cancer couldn’t survive and would go into apoptosis or be destroyed. Now what those researchers in did was: they took a Listeria strain and modified it in a way to incorporate radioactive 188-Rhenium. Then they injedcted those modified cells into mice with pancreatic cancer.
And now it’s getting awesome. The bacteria are killed by the immune system of healthy cells, but can invade the immune suppressed cells of the metastases, sometimes even the primary tumor. By this 188Rhenium accumulates within the cancer cells to a degree that will effectively kill the cell and thus suppress furhter spreading and even reduce, possibly cure the actual cancer. Isn’t that cool?
Okay, admittedly, this is early stage research in mice. So it might not be possible to adapt that to humans. And it would still take years until it could actually be applied, not even thinking of the ethical and juristical problems that would arise from the pure idea of healing people by injecting them pathogens. But; we’ll never know, and in the end it could just turn out great.
Oh and one more cool thing about listeria: they look like comets when they move within the cells, or should we rather call it: little nuke-rockets? see the vid.
http://www.youtube.com/watch?v=mZbmywzGAVs
neanderthal skulls (Photo credit: leted)
http://www.youtube.com/watch?v=mZbmywzGAVs
Hey, Going to keep it short but I wanted to post a little something ahead of the weekend for you to chew on, and I found this little piece of candy.
I stumbled on this by pure chacne, but wow did it struck me!!! this could, to my belief very well lead to one of those, great, little paradigm shifts that keep science where it belongs, at the edge of knowledge, driven by constructive self-criticism.
with that, have a nice weekend everyone
Scientific scribblings. “So sorry, that this sound somewhat silly.”
I am a scientist. Admittedely, I’m starting this one up with a slight notion of self-obsession, some almost superficial narcissism, but it is what I am. And as a scientist, I sometimes do all this crazy, weird, and interesting scientific stuff, the world needs to hear about. And that is just the point. The world needs to hear about this stuff. So the main object for scientists should not be committing experiments and brooding over data in small – shelter-like – offices, shared with other similar minded sufferers. Instead it should be about communicating science. I know of a guy who was doing just that; observing nature, doing experiments somewhere in the northern norwegian wilderness. But, although he was doing some fine research, he never turned out to be a scientist, soleley as he didn’t communicate and shared what he was doing. No external input, no allowance of criticism and no chance to aid others in their day to day struggle, trying to solve those greater misteries we encounter every time we open our eyes.
With that being the first stroke in the picture I’m trying to draw, while you are watching, lets clean our brushes and start bringing in some background colouring.
Science is about communication. And if communication is our canvas, then our words and writings are the colours we use to express what we see so clearly in our minds. And whoops, there we are already, right at the core of the biggest problem I see in scientific writing. Way too often, people are colourblind, or restrict themselves to drawing in black and white. And as I may add, they even avoid mixing those two, in order to at least add some fourtynine shades of grey, given a standard variation of around 1, witth a single-directional effect, and a 10% confidence level.
And among all those monochromatic drawings, you’d imagine some colourfull images would stand out, well I guess they would, but first you would have to find them, pick them up and remove all the covering cloth, that we are so used to use ,willingly wrapping up our work, whishing someone would only publish it that way.
Why would we do that? you may ask. Well, because publishing only happens after reviewing, accepting and a whole lot of back and forth-ing (I’m not even sure that word exists, but I’m sure you get my point). And among all those people who observe and judge our pictures, it is almost certain that there is at least one who’s blind to bright, beautiful colouration. And as we are so frightened of rejection, despite the fact that we should have grown custome to it ages ago, we give in. And we take what we created, we put it on a black and white copying machine, and push the button…voila, something acceptable to that crowd of grey authorities we try to impress.
But we lose everyone else. We lose our primal intention: To astonish people, to have them see, have them wonder, and maybe even inspire them.
A final note from the author: This text will (NOT) be reviewed, revised, and/or edited in accordance and intention to match the commonly accepted litterary means of what is generaly understood as “Scientific writing”
Does size really matter? or what “save the whales” doesn’t tell you about the microcosm
Red blood cells on an agar plate are used to diagnose infection. The plate on the left shows a positive staphylococcus infection. The plate on the right shows a positive streptococcus infection and with the halo effect shows specifically a beta-hemolytic group A. (Photo credit: Wikipedia)
Yesterday I, once more, found myself trying to explain my work. Usually that ends up being some kind of rather nerdy conversation, typically including something like “it’s actually more interesting then it sounds” or “you know I really don’t want to bore you with that”. The usual thing you could say. And as always with that symptomatic self induced doubts all scientists have about their work. Which is good. If we wouldn’t have doubts on what we are doing we couldn’t assess errors in our hypothesises if we encounter them. Although it’s not quite the optimal thing when it comes to PR-work, given that this attitude is usually not likewise shared among shareholders.
However this time, their was a slight twist in my trials of explanation. That was the backround of the person sitting opposite to me. She had a little more of a medical view on microbiology while I’m clearly more into the whole (switching to a Tim Minchin voice) Environment thing.
So what was that little problem I came across? – It was the main question we environmental microbiologists always ask, and around which our whole lives circle. – Who is there, and what do they do? – and quite regularly we already fail at answering the first question.
In medical microbiology it’s usually a little bit different. At least many more of the bugs you encounter there can be cultivated, isolated, sequenced and tested for all those little things one wants to test them. And much more important, by this means they are clearly defined as Vibrio something, Yersinia somethin, Neisseria something and so on.
In environmental microbiology, though we apply the same idea of a species, we usually have no idea how to cultivate them, sometimes it’s not even possible, and thus have to rely on different techniques to get our informations. However, it’s not as easy as doing a gram- staining, incubating some blood agar and doing some tests and then ultimately pin pointing it down to that one species of bacteria (I don’t want to minimalize the work my colleages are doing with this little exaggeration, so please, no offence ment)
But what is a bacterial species? (And if by chance I haven’t lost you by now, good thing, now we’re getting to the melting point of it, so get excited.) Conservatively spoken, a bacterial species is defined by a threshold of 97% sequence identity within the 16Sr DNA gene, with 90% defining the genus level. Lets put that in numbers, just for the fun of it. That means that if within the 1500 nucleotides of the 16Sr DNA gene 1455 are identical it is still the same species. And we are only talking of one single, rather conserved gene here and still we allow for 45 differing positions and still call it one species. Lets extrapolate this a little. I think it is commonly known, that humans and chimpanzee differ by roughly 1% within their whole genome. And that, once again, really struck my mind. If we would apply that idea in general, then I guess it would be totally valid to assume that on planet earth there would be around one genus of monkeys, with maybe two or three species. (I don’t really have the numbers here, so be forgiving) And that would just continue on and on like that, and all that diversity we so desperatly try to sustain would vanish in a haze of name calling and phenotyping. And it wouldn’t stop there. With diversity decreasing so drastically we would really have to reconsider things. I could only imagine the WWF for example, being forced to reduce so drastically, that it would have to give up both it’s double-U’s and would be left there with a big capital F!
Now that would be horrible, because no one would be left or care to save the pandas, the polar bears, the cute little seals and beware, the whales. But really, no one gives a s… about bacteria, they dissappear on a daily basis, and luckily quite a lot appear about the same rate. Especially so, since we cannot really distinguish whether we are dealing with just a phenotype or two different species, based on our crude assumption of species concept.
And furthermore, we do not even have the slightest idea of how many species we are actually talking of here, there use for human society completely set aside.
Yet, I do not have a solution for all of this, but I’m deeply admiring the problem.Oh and here’s something to read a little further if you still care to, after my little rant.
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20133a.html
So enjoy, and don’t forget, bacteria (and archaea) want to be protect just as the fish in the ocean, and the polar bears.
Microbegeek 