Imaging the Microscopic World

One of my best friends, who I've known since 1st grade, is currently in med school in NYC. He came back around recently & we always talk in depth about scientific topics. We were discussing the crazy things that happen in the small scales of microbiology.

On of the most underrated uses of the computer is as a visualization tool. Digital media can allow us to conceptualize processes existing on levels that we can't directly perceive.

I thought the animation in this TED talk by Drew Berry, showing the molecular workings within our own cells, was pretty mind-blowing.

Drew Berry: Animations of Unseeable Biology 

Since I'm talking about small-scale phenomena, I'll also post this almost surreal video of tiny organisms in water.

Even though the narrator talks like some kind of robotic alien, the video of the microscopic creatures is amazing.  Turn off the sound & put on Groove Salad instead.

Microscopic Worlds

It makes me wonder... what in the world is going on with this very weird thing we call "Life"?!?!

Microbial Meditations

This weekend my friend who I've know all my life & who's going to med school in NY, was in town. We basically stayed in his pool & drank beers all afternoon on Saturday, when the temp was 100º+. We always have great conversations & now he's becoming even more knowledgeable about medicine & science, in general.

Some of our talking about physiology & also the microscopic world made me think of a few articles I've seen recently. They're about micro-organisms, the tiny lifeforms that make up most of our 'being'.

Wikipedia:

Composition of the Human Body

We "human beings" are more of an ecology of life, rather than 'individual' entities.

NYTimes:

In Good Health? Thank Your 100 Trillion Bacteria

Bacteria aren't the only symbiotic life forms within our skin...

Gizmodo: 

The Weird Fungus That Lives In Your Gut

Here is a clickable graphic, showing the various things throughout our body:

Scientific American:

 Explore the Human Microbiome [Interactive]

On a more disturbing note, there's evidence that micro-organisms may also be able to directly effect a more complex animal (like a human).

 Raw Story: 

Studies Suggest That Microbes Can Control Our Minds

People gave George Lucas alot of crap for adding the 'Midi-chlorian' concept to the Star Wars universe, but I thought it was an interesting angle. The idea of trillions of tiny, living things creating energy fields that can be sensed or manipulated is an explanation that mirrors the vital necessity of these unseen organisms in the real world.

One thing I love about modern computing is the ability to visualize the reality that lies beyond our immediate senses. There've been many animations created that make processes on the cosmic & microscopic scales able to be easily understood. 

This is a good video showing the life of the dreaded flu virus:

Finally, here's a remix of a Bjork song I came across while searching Google for things in this post. Leave it to her awesome craziness to write a song comparing love to a virus.

The Human Being is an Ecosystem

a bacterium... on a diatom... on an amphipod

I've been seeing alot of interesting articles about the billions of micro-organisms that make up our body.

Even though we spend our lives thinking of ourselves as individuals, singular beings... we are actually walking ecologies, full of tiny creatures inside & out.

The fact of the matter is that each of us contains more bacteria than human cells!

Through new imaging techniques & computer graphics, technology is allowing us to visualize the complex microscopic worlds contained within the body:

XVIVO Scientific Animation

 Daily Mail:

Breathtaking Animated Simulations

 of the World Within the HUMAN BODY

Despite being a fairly neat person, I'm not really a germaphobe, so none of this information really bothers me. It's just the way things are, & nobody can be a fully-sanitized, immaculately clean person.  With that in mind, here's some headlines that may fascinate you, gross you out, or both.

BBC:  

Feet Home to More Than 100 Fungi 

Smithsonian Magazine:

Microbes: The Trillions of Creatures Governing Your Health


Design you Trust;

Your Daily Tech Habits are Making You Sick

(Infographic)

Microorganisms in our body may also be affecting our thought processes, in ways we don't fully understand:

Sci-News:

Study Reveals Changes in Gut Microflora 

Can Affect Brain Function

There is also a mystical aspect to the idea that our bodies are communal biological vessels, teeming with life throughout.

Prehistoric Shamanism:
We Are Not Alone: 

The Shamanic Implications 

of Our Body’s Microorganisms 

Alot of people criticized George Lucas's revelation in the Star Wars prequels- that "The Force" was actually a field that interacted with tiny organisms called Midichlorians. I thought this was actually a good way to explain the mechanism behind Force-sensitive beings. This symbiosis mirrors the interaction between life on the macro & microscopic scales in the real world.

What we should try to understand is that Life is infinitely complex, & the deeper we look into its processes, the more questions will arise. We have alot to learn about the processes in even the simplest forms of life:

Wired:

There’s No Such Thing as a ‘Simple’ Organism

Finally, here's a way of looking at our symbiosis with microbes that might be more creepy than comforting:

seen on Cheezburger

"Small World" Photomicrography

I am endlessly fascinated by the complex world of which I am a part.

There are infinite continuous levels of reality- from the spectrum of the cosmic phenomena of the very large, to the tiny features below our threshold of perception.

The Monkey Buddha Archives:

Microscopic

With advances in technology & photographic techniques, it is now possible to visually experience things that have never been able to be seen before.

On this isn't happiness, I saw some awe-inspiring photos from Nikon's photography competition that focuses on microscopic phenomena.

Nikon:

Small World Photomicrography Competition

 The website has galleries of entries going back a few decades.

Here are a few of my favorite images from this year's competition:

Conochilus unicornis (rotifer), actively feeding. (Charles Krebs, Washington, USA) 

 

 

Ceriodaphnia sp. (water flea). (Rogelio Moreno, Panama)

 

 

 Paramecium division. (Arturo Agostino, Italy)

 

 Ant eye. (Noah Fram-Schwartz, Connecticut, USA)

 

Hidden Life of the Cell

 

This past weekend, I watched a BBC documentary that I had been wanting to see, Our Secret Universe: The Hidden Life of the Cell.

The Hidden Life Of The Cell from Dominique Cressatti on Vimeo.

It explained the biological processes that take place in a human cell at the microscopic scale. Specifically, the show followed the journey of an adenovirus as it tries to propagate & infect the body by taking over our cells.

I love science, anatomy, & biology- especially what is going on at the level below the threshold of our senses. The idea that there are all these organized processes and synchronous activity going on trilions of times at the cellular level, throughout any individual's body, is too much to wrap one's head around.

To me, being able to visualize these scenarios is key to understanding them. That is where modern methods of computer animation become so important. Being able to accurately render these microscopic phenomenon using 3D graphics allows us to appreciate the wondrous reality of our own bodies at such a small scale.

It reminded me of another video I've posted that similarly showed the workings of our cellular biology:

Life Inside a Cell

iThink Tech 2015

In my last post, I shared a project from my college years, called the Omega Computer.

"Omega Computer" Concept

The project assignment was to design a computer of the future. Years later, I revisited the challenge of imagining futuristic computer technology & took it a step farther.

Instead of the external, portable devices used in the Omega Computer concept, I designed a computer brain implant called the "Apple iThink". You can see the specs of the iThink in my original post:

Apple iThink- Upgraded

Since I made those graphics, I've closely followed developments in science and technology that are leading toward a brain-computer interface, like the iThink.

I see technology, like my iPhone or computer, as extensions of my mind. The mystic sentiment that "consciousness is in all things" seems more true, the more I look into Reality. The Universe is made up of something more fundamental than particles or atoms- The Universe is made of information.

Human consciousness is just one manifestation of the Universal Information Field (UIF), that can manifest in infinite varieties. There is no reason why the ordinary conscious experience of the biological brain cannot be modified or enhanced to create novel states of being.

Of course, every step of the way there will be problems and questions that have to be addressed. Certain choices and directions may have unintended or negative consequences. However, I think it is inevitable for humanity to continue to seek new abilities, information, & understanding. We have uniquely mastered technology for this end, and will continue to expand both the individual and collective consciousness through technological means. Perhaps suprisingly to some, this technological innovation will be continue to be simultaneous, and perhaps symbiotic, with deeper spiritual and philosophical understanding about the nature of ourselves and our world.

I've collected links which, individually, are amazing developments. However, when seen as precursors to technologically-augmented consciousness, these scientific breakthroughs signal new frontiers in the human experience.

Time:
• 2045: Kurzweil on When Humans, Machines Merge


New Scientist:
• Cyborg Tissue is Half Living Cells, Half Electronics

Extreme Tech:
• MIT Creates Glucose Fuel Cell to power Implanted Brain-Computer interfaces

Daily Mail:
• The Groundbreaking Microscopic Thread That Could Let Us Plug Our Brain Into a Computer

Waking Times
• Decoded Neurofeedback: Matrix-like Learning With No Conscious Effort
 
Extreme Tech:
• Brown University Creates First Wireless, Implanted Brain-computer Interface

The White House:
• BRAIN Initiative Challenges Researchers to Unlock Mysteries of Human Mind

Kurzweil AI
• Organic transistors for brain mapping

Popular Mechanics:
• Going Wireless and Restoring Memories: The Incredible Future of Brain Implants

CNet:
• What Google Glass Aspires to Be

Technooccult:
• DARPA Wants to Fit Soldiers with a Little Black Box Brain Implant

The Atlantic:
•  The Not-So-Distant Future When We Can All Upgrade Our Brains

DefenseOne:
• The Military Is Building Brain Chips to Treat PTSD

The Verge:
• Google Leads $542 Million Funding of Mysterious Augmented Reality Firm Magic Leap

Techcrunch:
• The Ongoing Quest For The ‘Brain’ Chip

H+
• Biology is Technology — DARPA is Back in the Game With A Big Vision

BBC Future:
• The Code That May Treat Blindness

Smithsonian:
• A Flexible Circuit Has Been Injected Into Living Brains

Aeon:
• Hive consciousness: Do We Really Want to Fuse Our Minds Together?

Tooth Zoom

I came across a mind-bending animation- which zooms into the surface of a tooth at increasing degrees of magnification, down to the atomic scale:

This virtual journey through scale demonstrates the fractal nature of reality.

The world is not a set of discreet levels- such as the cosmic, human, microscopic & atomic scales. Reality is a non-stop continuum of infinitely intricate detail.

I also found a video version of it on YouTube:

Molecular Visualizations of DNA

As another birthday approaches in my life's timeline, I am in ever-increasing awe of the miracle of both my existence and that of the Universe as a whole.

The older I get, and the more I learn... the less sense anything makes! As my mind opens up to the infinite nature of reality, the explanations of the world's phenomena pale in comparison to the mysteries whose surface they barely scratch.

In traveling up and down the World Tree through all levels of existence, there are wonders at every scale of dimensionality. Contemplating the processes going on at the microscopic and quantum levels really cause my mind to short-circuit.

Visualizations through computer-generated graphics have allowed us to access secrets of the Universe in ways that were previously unimaginable. Especially in the realm of molecular biology, we are now able to model details of our own anatomy on the tiniest scales that give us deeper insights into the amazing circumstances that form our being.

This video by the Walter and Eliza Hall Institute of Medical Research give us a mind-expanding glimpse into the continuous activity of DNA that is going on in every one of us, trillions of times throughout all our cells, at every moment. It's completely crazy, and the complexity of it all is incomprehensible in its totality.

Here is another high-definition animation by the institute, with more footage, but no narration. All I can say is WTF! How can you watch this and not have your jaw drop in astonishment?

As a side note, I totally believe that the accounts of crystalline, scintillating light serpents by shamans in trance states are their experiences with their consciousness being transferred down to the level of DNA. They are interfacing with their own genetic code on a molecular and perhaps sub-atomic level.

The Monkey Buddha Archives:

Book Review: The Cosmic Serpent

Life is Strange

Thousands of Strange Creatures
Found Deep in Ocean

I've always thought that self-perpetuating life probably exists in other places throughout this relatively infinite Universe. However, I also think that beings from other world wouldn't necessarily physically look like us at all.

Sending messages to the stars or trying to communicate would suddenly seem ridiculous if alien life appeared & floated out of a spaceship looking like the sea cucumber in the photo above. We would be in no position to expect direct communication with abstractly weird beings from another world. What if they didn't deal with sound or light at all, but communicated & navigated using subtle manipulations of gravity fields? We wouldn't even know they were sentient without evident technology.

On the other hand, it's possible that space/time traveling aliens would be able understand us- like we are deciphering communication between bees & other animals. If there are alien beings advanced enough to be visiting us, they probably see Earth like a zoo & just use their 4-dimensional technology to pop in & out of our world like people drive a jeep through a safari.

UFO's aside, It's amazing to see all the new images of life that science and new technologies are discovering on all scales. This is a set of microscopic images that I saw on io9 that is crazy:

Algae Sex and Amoeba Smackdown
Best Microscopy Videos of the Year

The videos, like algae dividing, are almost surreal. These things are happening everywhere & at all times around us, but seem really strange because they exist on a scale beyond our immediate perception. Here is the full gallery from the Olympus Bioscapes contest:

Olympus BioScapes
2009 Winners Gallery

Unicellular Algae

The Flower of Life: Pattern of Creation

It's a New Year! It's a time where we mark a new beginning.

The circular 'Flower of Life' was a metaphorical symbol for Creation & Genesis in ancient cultures.

\When I chose to use it as a basis for the game "Da Vinci's Challenge," I realized it was more than just a cool design for a game board. The seemingly simple pattern of circles has many deep symbolic meanings, which have been contemplated & studied throughout human history.

Monkey Buddha Archives:
Da Vinci's Challenge

 
Here is the geometric construction of the circular Flower of Life symbol, compared with the formation of galaxies and embryonic cells.

The Flower of Life contains mysteries that span time & space, from the microscopic to the cosmic levels.


Graphic seen on:
Awakening Our Truth

Small World Photography 2015

The invention of the microscope opened up a new level of reality that was previously outside the realm of human perception.

Since then, we have been continuously expanding our boundaries of experience, using tools that help us to understand reality at different scales and in different modes. It's possible to see things that people in previous times not only were unable to see, but were unable to even imagine.

I've posted before about the Nikon Small World photography contest. It is a contest that combines science and art, with entries of photos which show fascinating images of mostly biological systems & phenomena in the microscopic realm.

The Monkey Buddha Archives:

"Small World" Photomicrography

On Neatorama, I saw the winners of this years contest. The winner was this awesome closeup image of the compound eye of a honey bee, covered in particles of pollen.

To see the other images, check out the site for the contest:

Nikon's Small World

2015 Photomicrography Competition

Book Review: "The Cosmic Serpent: DNA and the Origins of Knowledge"

 While I was on my honeymoon earlier this month at Cape May, I brought along a book to read on the beach that as been in my queue for awhile.

"The Cosmic Serpent: DNA and the Origins of Knowledge"

by Jeremy Narby

The author Jeremy Narby begins the book with the mystery of ayahuasca- a powerful psychedelic brew originating from the jungles of The Amazon in South America. This botanical, mind & soul-altering concoction is created from a combination of the Banisteriopsis caapi vine, which contains several alkaloids that act as monoamine oxidase inhibitors (MAOIs). The other ingredient, a shrub Psychotria viridis,  contains the primary psychoactive compound, dimethyltryptamine (DMT). The MAOIs from the B. cappi are required for DMT of the P. viridis to be orally active & produce the visionary experience.

The question that has presented itself is- how did the indigenous tribes know how to combine these two plants, out of thousands in the jungle, to create a specific chemical reaction to create the desired effect? The ayahuascero shamans claim that the plants themselves revealed this truth to their ancestors.

This idea of some kind of intelligence in the plant relaying this information creates another question- one that is the main premise of this book: Can ALL life communicate on levels (down the cellular and molecular scale) that science might not be currently aware of, & that does not involve the use of symbolic language that we humans are familiar with? Could the DNA molecule itself, besides being an encoder of information, also be capable of communicating and transmitting information, even perhaps somehow into the level of consciousness?

In ayahuasca trances, glowing, vibrating snakes and serpents imparting knowledge are a common motif. The author investigates whether these might be visualizations of the continually pulsating, light-emitting  DNA strands themselves, somehow communicating information to the emergent neurological phenomenon that we recognize as the human mind. Perhaps it also goes the other way, and our mind when unlocked in a certain manner can be transported down to directly interact and perceive at the scale of cells and molecules.

  Serpents by TAS Visuals

The Newtonian mechanistic view of the Universe, especially when it comes to life, is completely inadequate for having a true, holistic view of the world. However despite the awe-inspiring intricacy of life at the microscopic scale & weirdness of phenomena at the quantum level, science still has trouble grasping with the ephemeral nature of mind and consciousness as anything other than brain activity. This is understandable, since it is hard to quantify the idea of a universal consciousness, patterns of coherent energetic information transmission that exist EVERYWHERE- pervading all aspects of this Universe, at all scales..

This is the axis mundi that I have already mentally traveled up and down many times, and was guided through once again by the author as he connected the systems & processes of life from the microcosm to the macrocosm.

Underlying this quest that the author has written about, is the idea that the wisdom and traditions of native people should be preserved along with their land & environment. The profit-driven juggernaut we call the pharmaceutical industry cannot be allowed to exploit healing knowledge and plants that exist for the benefit of everyone. Although science should have the freedom to learn and understand as much of our reality as possible, that knowledge should not be used to restrict and refine discovery for the selfish gain of soulless megacorporations.

I enjoyed reading The Cosmic Serpent, and it was the perfect mix of science and mysticism for a syncretist such as myself. It made me think deeply about biology, spirituality, ecology, anthropology, and the complexity of life & reality itself. It was a relatively short book, but full of mind-expanding insights and information that I'd highly recommend.

3D Model of Brain Cortex Cells

There are few technologies that have been as useful for advancing our understanding of the world as computer imaging & 3D modeling.

Using computers and software to simulate previously unknowable systems, we can visualize phenomena from the microscopic to the cosmic scale. One area where these visualizations are extremely helpful is in biology and anatomy. The human body is an extraordinary collection of parts & processes, and there are aspects of it that can only be experienced through computer simulation.

I recently saw this article about the imaging of a small slice of a mouse's brain neocortex, or gray matter.

Huffington Post:

These Stunning Images 

Will Take You On A Journey Through The Brain

The neocortex is the outer area of the brain that is responsible for complex information processing. The area of brain tissue that was studied was smaller than the cross-section of a human hair, and was sliced up into extremely thin slices. The slices were scanned & the area was reconstructed digitally, so it could be analyzed in precise detail.

The imaged area was based around two nerve cells, and included all the other cells that intersected that densely-packed space. The different cells are encoded using colors to differentiate them. The awesome thing about having a digital model is that the various elements can be separated, isolated, and manipulated to understand their different aspects.

I am fascinated by these kinds of studies and the insight they give into ourselves & the incomprehensibly complex nature of our bodies.

Here is a link to the study from Harvard University:

Cell.com

Saturated Reconstruction of a Volume of Neocortex

This short video gives a concise description of the study & the visual representations of the cortical tissue.

Neuroscience: Crammed with Connections 

 

I've previously posted about the complexity found within single one of these brain cells.

The Monkey Buddha Archives:

A Look Inside a Brain Synapse

 Reality consists of infinite layers of endless detail, that exists on all scales

Panspermia: Life from the Heavens?

Scientific American:

"Did Life Come from Another World?"

I was watching a show on the Discovery Channel about meteors (also known as shooting stars), pieces of cosmic debris that can range from the size of a speck of dust to the size of a boulder.

The show touched on a theory that I have heard before called "Panspermia." Essentially, the theory is that microbial life can survive and be transported through space on meteoroids. Certain bacteria and fungus spores have been proven tough enough to survive the vacuum & temperature extremes of outer space.

As they were discussing this, they showed a video of a meteor approaching Earth, and I saw a fascinating fractal visual relationship to microscopic images of human fertilization that I've seen.

Another physical explanation for the generation of life is the primal energy of lightning fusing molecules into complex forms that result in rudimentary, yet energetic and self-replicating processes known as life.

The similarity of form between all 3 destructively creative events is evident in their profound simplicity, the merging of the two most basic forms recognized by human consiousness... the line and circle:

I remember a different show I was watching about early Christianity, and on an ancient stone wall they had drawn a Vesica Piscis in the form of the 'Jesus Fish' and a Cross. I realized that Christianity had two of the most powerful symbols known to man. Here again, symbolically, are the merging of the basic forms of the circle and the line, which are the essence of our mind's visual organization:

Template for the Flower of Life,
the metaphor for the self-replicating nature of living things,
containing the secret of the 'Jesus Fish' in red.
(click)

Animating The Cellular World

On Visual News, I saw animations by Markos Kay that I thought were really cool. I am endlessly amazed by the study of Life, biology, & things on the microscopic level that we can't perceive with our ordinary senses. These animations simulate biological processes on a cellular level & look almost psychedelic.


The Flow from MRK - Markos Kay on Vimeo.



These videos show the "squishiness" of life on the cellular scale. Everything is vibrating and interacting. Life is much more full of "life" than we realize. I think these animations capture that vibrant & organic quality.

The Powers of Ten: Lymphocyte from MRK - Markos Kay on Vimeo.

On a side note, I've been listening to alot of lectures by Dr. Bruce Lipton. He thinks that environment is much more influential than genetics for the organsm. DNA is just a blueprint, but he explains that the real "brain" of the cell is the membrane. This is where interactions take place that influence the response of the cell. It is where the cell body "learns".

Autumn Leaf Macro Photo

 Macro photo of a multi-colored autumn leaf. 

Nature Photography

by Paul Micarelli

 
The fractal contrast between the green & red, with yellow in between, is so vibrant.

Then you look closer and see the microscopic texture, and realize that there are millions of cells working as a system & forming this structure...

We exist in a practically infinite continuum of scale, from the quantum to the cosmic... (and this doesn't even include other dimensions that may be outside our ability to experience or comprehend, at all).

Hidden World: Zen Pond

I saw this video on MindTV & was mesmerized by the views of various microscopic lifeforms.

The zen-inspired music adds an introspective quality to the footage of the life that exists all around us, but is unnoticed by our normal perception.

Hidden World: Zen Pond

Zoomable Cell Sizes

One great thing about the computer as a learning tool is the ability to create interactive content that let's you experience ideas in a engaging way.

Information Aesthetics linked to a site by the University of Utah Genetic Science Learning Center that is a zoomable scale of microscopic entities. I thought it was a really insightful tool to experience the relative sizes of things to small to experience directly.

Cell Size and Scale

Our Bodies are Ecosystems

Discover Magazine: "Your Body's A Planet"

I've posted before about the bacteria and organisms living throughout our bodies, but it never stops amazing me how the body is mostly a vessel for an entire universe of living organisms.

90% of our mass supposedly consists of living microbes, viruses affect our DNA, and we cannot live without organisms like stomach bacteria. The idea of an independent 'self' is ultimately just that - an idea. Each person is really a system of symbiotic beings in constant interaction, on many different scales.

The amount of integration and effect that microscopic life has with us makes George Lucas's idea of Midichlorians not quite as stupid as I first thought...

Mmmmpph! Antibacterial soap... useless, it is!!!

The Brain in Our Belly

I have always had a deep interest in biology & anatomy. The more I learn about living systems, the more I am utterly amazed.

Recently, I have been particularly curious about our digestive system & the details of its workings on a microscopic level. I have been posting about the connection between the microorganisms in the gut and how they affect us, without us even being aware of its influence. The microbes in our digestive tract can affect our metabolism, food cravings, and even our mood or personality traits.

The Monkey Buddha Archives:

Gut Microbes

I saw this informative post about another important aspect of our gut that we don't think a lot about, even though it is our "second brain". I'm referring to the complex array of 500 million nerve cells that line our digestive organs, called the enteric nervous system, or ENS.

neurosciencestuff.tumblr

Gut Instincts: The Secrets of Your Second Brain

This system of nerve cells in our gut are not only responsible for controlling digestion. It is also being found to have complex effects on our overall physical health & mental states.

The ENS is a part of our unimaginably complex feedback loop of physical & chemical stimuli that regulates body function. The chemical processes controlled by these neurons in our gut include the creation of hormones & neurotransmitters.

This is important because the creation of neurochemicals such as serotonin (the "feel good" molecule) & dopamine (the "pleasure & reward" molecule) by these cells could affect our physical sensations & perhaps even our personality or mood.

As we gain more knowledge about the intricately interconnected nature of all these subtle systems in the human body, we will also gain better insight into all aspects of the human being. Disease, mental disorders, physical ailments, and the keys to healthy & happy living will all be understood better.

This will lead to an ever-improving quality of life for people who are willing to take steps to improve their interaction with their own body. This can be done through better diet and healthier lifestyle, as a result of more conscious attention to the workings of our wonderfully complex biological systems.