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The Illusion of Reality
In 1999, a movie came out which blew everyone’s mind, and still twists our brains today : the Matrix. It described a future where reality is an illusion, a computer-simulated universe in which we thrive. Solipsism with guns in a post-apocalyptic world. But what if I told you… they’re right ? In fact that’s not true, they’re probably completely mistaken. Reality is not a computer-generated dream. Reality is empty. Well… 99,99% empty.
Science basics, matter is made of atoms. Atoms are themselves made of a cloud of electrons orbiting a dense nucleus of protons and neutrons. Separating electrons and the nucleus is just air. Not even air, since air is composed of molecules. This is why I can say that atoms are mostly empty, and therefore matter is mostly empty. We’ve known this for a very long time. Most of us would just give up and say “matter is nothing, so why bother ?”. Most of us, but not scientists. Scientists have twisted and mangled these teensy balls of nothing. They stripped these minuscule objects apart and threw the remains into a 27 kilometers collider to blow them up. They’ve invented machines and probes to witness matter in its very extreme intimacy. In 1951 they invented the Field Ion Microscope and they’ve taken pictures… of individual atoms. Repelled ions looking like clusters of stars or ripples into the nothingness.
So, why bother ? That’s why. Matter is almost empty. But we were here, and we took pictures to prove it.
Picture : Examples of field ion micrographs of (a) iridium, (b) a Pd40Ni40P20 bulk metallic glass, (c) a decorated grain boundary in a neutron-irradiated pressure vessel steel, and (d) 5nm-diameter secondary precipitates in the nickel-based superalloy Alloy 718
M.K. Miller (2000) The Development of Atom Probe Field-Ion Microscopy, Materials Characterization (44):1-2 11-27
- Agathe of Frontal Cortex

The Illusion of Reality

In 1999, a movie came out which blew everyone’s mind, and still twists our brains today : the Matrix. It described a future where reality is an illusion, a computer-simulated universe in which we thrive. Solipsism with guns in a post-apocalyptic world. But what if I told you… they’re right ? In fact that’s not true, they’re probably completely mistaken. Reality is not a computer-generated dream. Reality is empty. Well… 99,99% empty.

Science basics, matter is made of atoms. Atoms are themselves made of a cloud of electrons orbiting a dense nucleus of protons and neutrons. Separating electrons and the nucleus is just air. Not even air, since air is composed of molecules. This is why I can say that atoms are mostly empty, and therefore matter is mostly empty. We’ve known this for a very long time. Most of us would just give up and say “matter is nothing, so why bother ?”. Most of us, but not scientists. Scientists have twisted and mangled these teensy balls of nothing. They stripped these minuscule objects apart and threw the remains into a 27 kilometers collider to blow them up. They’ve invented machines and probes to witness matter in its very extreme intimacy. In 1951 they invented the Field Ion Microscope and they’ve taken pictures… of individual atoms. Repelled ions looking like clusters of stars or ripples into the nothingness.

So, why bother ? That’s why. Matter is almost empty. But we were here, and we took pictures to prove it.

Picture : Examples of field ion micrographs of (a) iridium, (b) a Pd40Ni40P20 bulk metallic glass, (c) a decorated grain boundary in a neutron-irradiated pressure vessel steel, and (d) 5nm-diameter secondary precipitates in the nickel-based superalloy Alloy 718

M.K. Miller (2000) The Development of Atom Probe Field-Ion Microscopy, Materials Characterization (44):1-2 11-27

Agathe of Frontal Cortex

science microscopy field ion microscopy history Frontal Cortex scientist in residence
Life Inside a Cell
Another week, another type of microscopy. Did you notice how much I like microscopy yet ? Even though, in biology, we have to rely on two major fields, imaging and molecular science. There are things you can’t comprehend in microscopy, just like there are things you can’t see in molecular biology. These are two sides of the exact same coin, and one must juggle between both to try and get some kind of understanding of what’s happening inside the cell. With microscopy, it’s easy to understand why it’s not perfect, why it unfortunately doesn’t hold all the answers. Most of the time, we’ve fixed an instant in time, the cell was living one moment, and was dead the next, stuck forever in what it was doing at the time. Looking into the objective, you can only see what was happening then. And even when doing microscopy on living cells, we mostly have to rely on specific markers, so all of what’s going on around is invisible. Unknown. And that’s without saying that a picture is just that, a picture, and sometimes you’re just baffled by what’s on the screen, just like when you see some abstract piece of art and think “What is this and why in the world is it worth $150,000 ?”
So we might develop wonderful technologies and extravagant techniques, just like the electron microscopy on “unroofed” cells you’re seeing here, we may well go further and further into getting details of what the inside of a cell looks like, we still have a bunch of work until we understand it all.
Still, it looks very, very cool.
Picture credits : Electron Micrographs of Unroofed Cells of D. discoideum, Immunogold Labeled for the Localization of Arp2/3 or the LimEΔcoil ProbeCells in the left panel expressed GFP-p41-Arc, which is marked by anti-GFP antibodies.
Till Bretschneider et al. Dynamic Actin Patterns and Arp2/3 Assembly at the Substrate-Attached Surface of Motile Cells. Current Biology, Volume 14, Issue 1, 6 January 2004, Pages 1–10
- Agathe of Frontal Cortex

Life Inside a Cell

Another week, another type of microscopy. Did you notice how much I like microscopy yet ? Even though, in biology, we have to rely on two major fields, imaging and molecular science. There are things you can’t comprehend in microscopy, just like there are things you can’t see in molecular biology. These are two sides of the exact same coin, and one must juggle between both to try and get some kind of understanding of what’s happening inside the cell. With microscopy, it’s easy to understand why it’s not perfect, why it unfortunately doesn’t hold all the answers. Most of the time, we’ve fixed an instant in time, the cell was living one moment, and was dead the next, stuck forever in what it was doing at the time. Looking into the objective, you can only see what was happening then. And even when doing microscopy on living cells, we mostly have to rely on specific markers, so all of what’s going on around is invisible. Unknown. And that’s without saying that a picture is just that, a picture, and sometimes you’re just baffled by what’s on the screen, just like when you see some abstract piece of art and think “What is this and why in the world is it worth $150,000 ?”

So we might develop wonderful technologies and extravagant techniques, just like the electron microscopy on “unroofed” cells you’re seeing here, we may well go further and further into getting details of what the inside of a cell looks like, we still have a bunch of work until we understand it all.

Still, it looks very, very cool.

Picture credits : Electron Micrographs of Unroofed Cells of D. discoideum, Immunogold Labeled for the Localization of Arp2/3 or the LimEΔcoil ProbeCells in the left panel expressed GFP-p41-Arc, which is marked by anti-GFP antibodies.

Till Bretschneider et al. Dynamic Actin Patterns and Arp2/3 Assembly at the Substrate-Attached Surface of Motile Cells. Current Biology, Volume 14, Issue 1, 6 January 2004, Pages 1–10

Agathe of Frontal Cortex

microscopy electron microscopy science biology actin Frontal Cortex scientist in residence
The Beauty of Fluorescence
Probably not a very good title, because I love fluorescence very very much, and I find it beautiful very very often. But today I’m going to talk about my favorite dye. 4’,6-diamidino-2-phenylindole or DAPI (cute name, in french we have a song which goes “Pomme de reinette et pomme d’api”, but anyway), is a fluorescent stain which binds to DNA. Therefore it is used in fluorescence microscopy to stain nuclei. It is particularly useful when applying multicolor fluorescent techniques, because the range of greens, yellows and reds sometimes makes it hard to distinguish between cells. DAPI’s blue makes a nice contrast, so we can never get lost.
Did I tell also that it’s the most beautiful thing to see in a microscope ? Because it is, it really is. Sometimes I have to remind myself I’m not looking at Avatar’s version of the night sky.
Top : Matt Benton. Two day old cricket embryo that has been partially separated from its egg. (zoo.cam.ac.uk)
Bottom : Dr. Heath Mills, Texas A&M University. Unidentified DAPI stained microorganisms within sediments as seen through a confocal microscope. (National Geographic)
Agathe of Frontal Cortex
The Beauty of Fluorescence
Probably not a very good title, because I love fluorescence very very much, and I find it beautiful very very often. But today I’m going to talk about my favorite dye. 4’,6-diamidino-2-phenylindole or DAPI (cute name, in french we have a song which goes “Pomme de reinette et pomme d’api”, but anyway), is a fluorescent stain which binds to DNA. Therefore it is used in fluorescence microscopy to stain nuclei. It is particularly useful when applying multicolor fluorescent techniques, because the range of greens, yellows and reds sometimes makes it hard to distinguish between cells. DAPI’s blue makes a nice contrast, so we can never get lost.
Did I tell also that it’s the most beautiful thing to see in a microscope ? Because it is, it really is. Sometimes I have to remind myself I’m not looking at Avatar’s version of the night sky.
Top : Matt Benton. Two day old cricket embryo that has been partially separated from its egg. (zoo.cam.ac.uk)
Bottom : Dr. Heath Mills, Texas A&M University. Unidentified DAPI stained microorganisms within sediments as seen through a confocal microscope. (National Geographic)
Agathe of Frontal Cortex
The Molecular Perspective
Scientific illustration is no easy task. Anyone who’s looked through a microscope and attempted to draw at the same time knows it. Try then to add some information to beauty, as to make the viewer be in awe and learn, and you’ve got a near impossible challenge on your hands. So if you’re familiar with scientific illustration, (or if you’re on Tumblr even,) you’re probably no stranger to David S. Goodsell’s work. Even then, it’s never a waste of time to talk about the best. And David S. Goodsell is certainly one of the best. He’s got the fantastic ability to combine hand-drawn illustration of intricate and complex biological mechanisms, accurate science, wonderful colors and great design, as to remind us that although cells are often represented as spheres full of nothing, they are far from empty.
Check out his website for more information and the gallery.
Above : This work was created as a commissioned project for Biosite. This view shows DNA being replicated in the nucleus. DNA polymerase is shown at the center in purple, with a DNA strand entering from the bottom and exiting as two strands towards the top. The new strands are shown in white. Chromatin fibers are shown at either site of the replication fork. 
Agathe of Frontal Cortex
Higher still and higher  
From the earth thou springest,  
Like a cloud of fire;  
The blue deep thou wingest,  
And singing still dost soar, and soaring ever singest.
    To a Skylark - Percy Bysshe Shelley
It looks like a painting or a very photoshopped picture of birds, but it’s actually an image taken in polarized light of crystallized glycine, tartaric acid and resorcinol. It was submitted by Edy Kieser to Nikon’s Small World Competition.
I’m thinking science, but I’m seeing art. I just love when that happens.
- Agathe of Frontal Cortex
Higher still and higher  
From the earth thou springest,  
Like a cloud of fire;  
The blue deep thou wingest,  
And singing still dost soar, and soaring ever singest.

    To a Skylark - Percy Bysshe Shelley

It looks like a painting or a very photoshopped picture of birds, but it’s actually an image taken in polarized light of crystallized glycine, tartaric acid and resorcinol. It was submitted by Edy Kieser to Nikon’s Small World Competition.

I’m thinking science, but I’m seeing art. I just love when that happens.

- Agathe of Frontal Cortex

(Source: artandsciencejournal.com)

science microscopy polarized light Nikon Small World To a Skylark poem frontal cortex scientist in residence
Data Visualization
"Data", that’s a scary word. All we can picture are mountains of numbers that are indiscernible from one another. But this is also a fact, entire genomes are getting sequenced, the universe is being mapped out… we’re entering an era of big data, even bigger mountains. So… what do we do with it ? We manipulate it, we design it, so that big data can be digested, dare I say enjoyed.
Sometimes it’s even fun to browse this mountain of information. At least that’s what I thought when I found the We Feel Fine project. This emotional search engine crawls blogs and networking sites, picking up sentences which include “I feel” or “I am feeling”, as well as the gender, age and location of the people posting those sentences. The result is a database of several million human feelings, sorted out, displayed, in the hopes of creating a piece of art for everyone, by everyone, sprouting from our deepest feelings.
Check out the java applet here.
- Agathe of Frontal Cortex
Data Visualization
"Data", that’s a scary word. All we can picture are mountains of numbers that are indiscernible from one another. But this is also a fact, entire genomes are getting sequenced, the universe is being mapped out… we’re entering an era of big data, even bigger mountains. So… what do we do with it ? We manipulate it, we design it, so that big data can be digested, dare I say enjoyed.
Sometimes it’s even fun to browse this mountain of information. At least that’s what I thought when I found the We Feel Fine project. This emotional search engine crawls blogs and networking sites, picking up sentences which include “I feel” or “I am feeling”, as well as the gender, age and location of the people posting those sentences. The result is a database of several million human feelings, sorted out, displayed, in the hopes of creating a piece of art for everyone, by everyone, sprouting from our deepest feelings.
Check out the java applet here.
- Agathe of Frontal Cortex
Data Visualization
"Data", that’s a scary word. All we can picture are mountains of numbers that are indiscernible from one another. But this is also a fact, entire genomes are getting sequenced, the universe is being mapped out… we’re entering an era of big data, even bigger mountains. So… what do we do with it ? We manipulate it, we design it, so that big data can be digested, dare I say enjoyed.
Sometimes it’s even fun to browse this mountain of information. At least that’s what I thought when I found the We Feel Fine project. This emotional search engine crawls blogs and networking sites, picking up sentences which include “I feel” or “I am feeling”, as well as the gender, age and location of the people posting those sentences. The result is a database of several million human feelings, sorted out, displayed, in the hopes of creating a piece of art for everyone, by everyone, sprouting from our deepest feelings.
Check out the java applet here.
- Agathe of Frontal Cortex

Data Visualization

"Data", that’s a scary word. All we can picture are mountains of numbers that are indiscernible from one another. But this is also a fact, entire genomes are getting sequenced, the universe is being mapped out… we’re entering an era of big data, even bigger mountains. So… what do we do with it ? We manipulate it, we design it, so that big data can be digested, dare I say enjoyed.

Sometimes it’s even fun to browse this mountain of information. At least that’s what I thought when I found the We Feel Fine project. This emotional search engine crawls blogs and networking sites, picking up sentences which include “I feel” or “I am feeling”, as well as the gender, age and location of the people posting those sentences. The result is a database of several million human feelings, sorted out, displayed, in the hopes of creating a piece of art for everyone, by everyone, sprouting from our deepest feelings.

Check out the java applet here.

- Agathe of Frontal Cortex

(Source: artandsciencejournal.com)

3 Photos
/ art science scientist in residence frontal cortex feelings big data data visualization

Biofilms

Bacteria, just by the sheer fact that they duplicate very quickly, and because safety is mostly in numbers, tend to form what are called biofilms. But biofilms aren’t quite just an aggregate of cells. These cells adhere to each other and to the surface, and produce an extracellular substance containing extracellular DNA, proteins and polysaccharides, that are going to act as a protective and adhesive layer. Some biofilms have even been found to contain channels to help distribute nutrients and signalling molecules.

So bacteria may well be able to survive on their own, but they are also able to intelligently organize their mass when difficult times arise, and we’re just beginning to see which dangers this can hold. To show these organization skills, researchers have tagged differents lineages of Bacillus subtilis — rod shaped bacteria commonly found in soil —  with distinct fluorescent proteins (TagRFP-T, sfGFP, TagBFP, mKate2 and mOrange2). They then mixed the cells randomly on a petri dish. By looking at the culture with a confocal microscope, they can detect the different colors used to tag the cells. Surprisingly, what should be a random mix of colors actually looks like an incredible painting, full of discernible streaks. Indeed, as the bacteria grew, they were found to organize themselves into patterns, reproduciblepatterns that can be predicted with mathematical models (Computational Modeling of Synthetic Microbial Biofilms, ACS Synthetic Biology). Therefore is looks like bacteria can arrange themselves so that the biofilm is divided in regions where cells exhibit different patterns of gene expression, to increase both their metabolic efficiency and their resistance to changes in their local environment.

The study of biofilms has skyrocketed in recent years due to the increased awareness of its efficiency and its effect on natural, industrial systems and human health. And it is far from over.

Photo credit: Fernan Federici, Tim Rudge, PJ Steiner and Jim Haseloff,  Haseloff Lab, University of Cambridge
This beautiful work was one of the winners in this 2012 Wellcome Image Awards

- Agathe of Frontal Cortex
Biofilms


Bacteria, just by the sheer fact that they duplicate very quickly, and because safety is mostly in numbers, tend to form what are called biofilms. But biofilms aren’t quite just an aggregate of cells. These cells adhere to each other and to the surface, and produce an extracellular substance containing extracellular DNA, proteins and polysaccharides, that are going to act as a protective and adhesive layer. Some biofilms have even been found to contain channels to help distribute nutrients and signalling molecules.


So bacteria may well be able to survive on their own, but they are also able to intelligently organize their mass when difficult times arise, and we’re just beginning to see which dangers this can hold. To show these organization skills, researchers have tagged differents lineages of Bacillus subtilis — rod shaped bacteria commonly found in soil —  with distinct fluorescent proteins (TagRFP-T, sfGFP, TagBFP, mKate2 and mOrange2). They then mixed the cells randomly on a petri dish. By looking at the culture with a confocal microscope, they can detect the different colors used to tag the cells. Surprisingly, what should be a random mix of colors actually looks like an incredible painting, full of discernible streaks. Indeed, as the bacteria grew, they were found to organize themselves into patterns, reproduciblepatterns that can be predicted with mathematical models (Computational Modeling of Synthetic Microbial Biofilms, ACS Synthetic Biology). Therefore is looks like bacteria can arrange themselves so that the biofilm is divided in regions where cells exhibit different patterns of gene expression, to increase both their metabolic efficiency and their resistance to changes in their local environment.


The study of biofilms has skyrocketed in recent years due to the increased awareness of its efficiency and its effect on natural, industrial systems and human health. And it is far from over.


Photo credit: Fernan Federici, Tim Rudge, PJ Steiner and Jim Haseloff,  Haseloff Lab, University of Cambridge

This beautiful work was one of the winners in this 2012 Wellcome Image Awards


artandsciencejournal A&SJ artsci artscience art science biofilm scientist in residence frontal cortex

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