CRISPR – human trials to begin

23 July 2016

I don’t know about you, but I’m properly terrified.

the TED talk on CRISPR was welcomed with muted applause, I expect due to the power of this new technology, and what we have, historically, done with greatly powerful technologies (see: plutonium). It seems rather quick to jump to human trials, considering how little we know about the technology, and its potential to spread out of our control.

From the Guardian

Crispr: Chinese scientists to pioneer gene-editing trial on humans

A team of Chinese scientists will be the first in the world to apply the revolutionary gene-editing technique known as Crispr on human subjects.

Led by Lu You, an oncologist at Sichuan University’s West China hospital in Chengdu, China, the team plan to start testing cells modified with Crispr on patients with lung cancer in August, according to the journal Nature.

Crispr is a game-changer in bioscience; a groundbreaking technique which can find, cut out and replace specific parts of DNA using a specially programmed enzyme named Cas9. Its ramifications are next to endless, from changing the color of mouse fur to designing malaria-free mosquitoes and pest-resistant crops to correcting a wide swath of genetic diseases like sickle-cell anaemia in humans.

Read the rest of this entry »

Life continues to define itself well past our extremest expectations

22 May 2012

Bacteria has been living on minimal oxygen all along.

While there are efforts to introduce a bill into Canadian Parliament to define the beginning of life, there appears to be new information that begs us to reconsider what we consider life in general to be. If we don’t know what life is, then how can we hope to define when it begins?

Despite this heavy-handed political approach to revisit the abortion laws in Canada, scientific study continues to turn up life in the most unexpected places (maybe they’ll discover some in Ottawa, if they look hard enough). Most recently, bacteria were found living in the 86 Million year old red clay at the bottom of the Pacific. It reminds us just how versatile our ancestors are, and how many of them are still with us.

the Articles

from Nature.comSlo-mo microbes extend the frontiers of life

Using so little oxygen that they barely qualify as life, the microbes, discovered by Hans Røy and his colleagues of the Centre for Geomicrobiology at Aarhus University in Denmark, have exceptionally low metabolic rates. And biomass turnover — the replacement of the building blocks essential to life — occurs only once every few hundred or even every few thousand years.

the abstract from Nature Magazine: Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay

Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. At threshold sedimentation rates of 1 millimeter per 1000 years, the low rates of microbial community metabolism in the North Pacific Gyre allow sediments to remain oxygenated tens of meters below the sea floor. We found that the oxygen respiration rates dropped from 10 micromoles of O2 liter−1 year−1near the sediment-water interface to 0.001 micromoles of O2 liter−1 year−1 at 30-meter depth within 86 million-year-old sediment. The cell-specific respiration rate decreased with depth but stabilized at around 10−3 femtomoles of O2 cell−1 day−1 10 meters below the seafloor. This result indicated that the community size is controlled by the rate of carbon oxidation and thereby by the low available energy flux.

article in Nature Magazine: Barely Breathing Microbes Still Living in 86-Million-Year-Old Clay

Scientists have discovered that deep-sea microbial communities, buried for 86 million years, are still consuming oxygen, albeit at extraordinarily low rates. These microorganisms eking out an existence in slow motion reveal just how little it takes to sustain life on our own planet, and potentially on others.

The scientists discovered that microbes can subsist on scraps of long-buried organic material because they consume it together with oxygen extremely slowly. Those living below 20 meters in the sediments of the North Pacific Gyre are consuming oxygen at a rate of 0.001 micromoles of oxygen per liter of sediment per year, the team reports online today in Science. At this rate, the microbes in 1 cubic meter of sediment would take about 10 years to consume the amount of oxygen the average person uses in one breath, says Tori Hoehler, a biogeochemist at the NASA Ames Research Center at Moffett Field in California who was not involved in the research.

Hoehler says that the research could inform the search for life on other planets. After determining whether an environment has enough water to support living organisms, he says, “these sorts of studies really address the next important question: Is there enough food for them to live?” Understanding life’s requirements for energy is key to determining the potential for life beyond Earth, Hoehler says. “They’ve taken a significant step in showing us, based on our own environments, what those requirements are.”

The findings also give Røy an appreciation for life here on Earth: “I find it so fascinating that you can take a cubic meter of mud and then store it for 86 million years, and somebody’s still living in it.”

Extreme Living

So-called “extremophiles” have been found in such inhospitable environments as those that are highly acidic or alkaline, extremely hot or cold temperatures, pressure, salinity, sugar concentration, under immense pressure, with little nutrients, and in the teeniest, tiniest of spaces. It’s quite incredible. Although most are microbes, there are a few that are multicellular, such as

213 Days to Dec 21st 2012

Up from the Depths, it’s… What is that?

15 May 2012

the Cascade Creature comes to say hello.

One of my pet peeves, and let’s not kid ourselves here, I have lots, is the phrase “now we know.” Somehow, this line suggests that our current way of understanding things is the final truth, that we will no longer need to question anything, for “now we know.” It’s also extremely dismissive of past ways of understanding things. It claims that whereas before we were mistaken, “now we know,” as if there is no chance that we are currently mistaken, or that yet another way of thinking will take over.

And just when we think we know it all, this happens:

220 Days to Dec 21st 2012

Mycorrhyza shouldn’t surprise ya

7 April 2012

The biological network – fungi, ,plants, bacteria, micro & macroorganisms.

Way back when, I lucked in to having a roommate who was an amateur mycologist (fungologist I suppose). He introduced me to morels, and let me peruse his library (including Magical Mushrooms Mischievous Molds by George Hudler). I have a degree in biology, yet there was never a course on mycology offered. Botany, sure. Zoology of course. But an entire domain of life was left off the curriculum. It was pretty disappointing. So I made up for lost time. It was completely fascinating.

(also, I’m making pasta with berbere mushrooms for lunch, hence the inspiration…)

Although Paul Stamets isn’t the greatest public speaker, he knows his stuff, and this presentation is astounding. Some of this stuff I knew, but a lot of it is new.

the Network

Fungi are pretty much hyphae, long branching structures that grow and branch in organic matter. Fungi are little biochemical factories, and they are responsible for decomposition. Mushrooms on a rotting log, or mold on your bread are accomplishing the same thing – decomposing the organic matter, and rendering it back to the earth. They also work wonders in a compost heap.

The mushroom part is the reproductive body, (fruiting body) of the fungus, and is a very small part of the overall organism. It releases its spores far and wide, and so continues the cycle of life.

As for the network, the hyphae join with plant roots in what is called the mycorrhiza (meaning fungus-root). The fungus benefits from the plant’s photosynthesis, and the plant benefits from the nutrients broken down by the fungus. Given that one mushroom can create mycorrhiza with several plants, and that plants can have mycorrhiza with several fungi, this interconnective symbiosis can spread as far as the local ecosystem will allow.

In Oregon, is a species of honey mushroom that is believed to be the largest living organism. It’s believed to have colonized the land over 9 square kilometres, and is thought to be about 2400 years old. I believe that this species is edible, and I’ve actually eaten something labelled “honey mushroom” from Oregon. I can only imagine that it was part of this ancient being. As this one entity is spread over such a vast area, what does the mycorrhizal network in Oregon look like?

Also, hyphae grow like nerve cells.

Fun with Fungi

before I forget, check out this Effective Microorganisms site – buy your own living goo to make your plants happier (and lots of other applications).

No idea what species these are, but they spontaneously appeared in a pot with a citrus tree – I fed them a blueberry.

From what I recall in my research, fungus are older than plants, closer in phenotype to animals, and were the original agent for the colonization of land (see lichens). Also, their spores can survive space travel, which some believe is how life on earth began. There’s so much to go on about, but I’d rather leave it with experts, such as the fine folks at the MycoBank.

Here’s some bioluminescent fungi.

theAbysmal Fungi

As you may recall (or not, who am I to judge?), the image below is called the Mycelium of Life, where the mycelium is the body of the fungus, i.e. a bundle of hyphae.

My thought was to remove the hierarchies associated with the various Trees of Life, and use something non-hierarchical. Mycelia are also an intrinsic part of the mycorrhizal network, which suggests interconnectivity as well as mutually beneficial symbiosis. It also suggests a connection with trees, i.e. the hierarchical, such that it is all inclusive and non-discriminatory.

The circles within circles of the above image are also like fairy rings, which suggests something magical, if not mystical (then there’s the whole magic mushroom thing, which is a whole other post entirely).

Mycelium of Life and the Maya Tree of Life

I’d read an account of a Maya myth regarding the tree of life, however, I haven’t been able to find the exact story again. The closest I’ve come is in the  Chilam Balam of Chumuyel (a book of histories, prophecies, myth, healing and so on with variations from village to village, hence of Chumuyel) in which the Gods plant trees according to the four cardinal directions to commemorate rebirth after destruction of the world. I imagine that the story I read also informed the image of the mycelium of life, and so I’ll paraphrase it as I recall (and it’s not such a bad story, I just wish I had the time to compose it properly, or at least find the original).

The Maya tree of life, as many others, has its branches in the heavens, its roots in the underworld, and the trunk is the earth. There are 13 heavens and 9 levels of the underworld, however both the uppermost level of the underworld and the lowermost level of the heavens are equivalent to earth. This corresponds to the 12 outer circles, 8 inner circles and 1 central circle in the Mycelium illustration.

The tree of life bore every fruit, nut and berry from its branches in great abundance. Animals flocked to the tree to feed on them. The fruit and nuts and berries fell to the earth, some to be devoured, others to disperse their seeds far and wide, to cover the earth.

The tree dies, or is destroyed, or is cut down (take your pick), yet four trees (one at each cardinal point) grow out of the earth, and like their parent tree, burst forth with all manner fo fruit, nut and berry.

The important point to all of this is the central point (whether it be a living tree or a stump) and the trees at the four cardinal points. With this image in mind, then the mycelium of life is more like an overhead (or underfoot) view of the trees, one central and one for each direction, interconnected by the mycelia/hyphae.

I imagine this story had some influence on the development of the mycelium image, however, as they both rely heavily on the four cardinal points, I assume that’s a good part of the symmetry. The 12 + 1 + 8 equivalence is unintentional (as far as I’m aware), and the 52 paths was also unintentional (but as 52 is a key number in Maya numerology, a welcome coincidence).

All this to say, the mycelium of life as a symbol bears much in common from the mycorrhyza of life, and as such, I’m happy to keep posting it around (even though I’m still not sure what it is, or what it represents – something to meditate on if necessary).

258 Days to Dec 21st 2012

Rhythms of Life

22 February 2012

Book Notes on Chronobiology and Photoperiodism.

Rhythms of Life – the Biological Clocks that Control the Daily Lives of Every Living Thing (2004) by Russell G. Foster & Leon Kreitzman

p2 “The big difference between us and other living things is that to some extent we can cognitavely override these ancient hard-wired rhythms. Instead of sleeping as our bodies dictate, we drink another cup of coffee, turn up the radio, roll down the car window and kid ourselves that we can beat a few billion years of evolution.”

“When [daily circadian rhythm] is disrupted we suffer from the relatively mild symptoms of jet-lag through to serious and poetntially life threatening conditions such as depression and sleep disorders.”

p3 “[Biological clocks]… are reset at sunrise and sunset each day to link astronomical time with an organism’s internal time.”

p5 “All of us in the developed world now live in a ’24/7′ society. This imposed structure is in conflict with our basic biology. The impct can be seen in our struggle to balance our daily lives with the stresses this places on our physical health and mental well-being. We are now aware of this fundamental tension between the way we want to live and the way we are built to live.”

[see Colin Pittendrigh]

p38 “Every atom in our bodies is oscillating at around 1016 Hz.”

“The rods and cones in the retina respond to light oscillating at between 1015 – 1014 Hz. The brain’s electrical activity…has a frequency of 101 Hz… The heart beats at approimately 100 Hz…and respiration occurs at about one breath every six seconds.”

p97 “Although at some level everything about a simple living organism is implied in its genes, on the other hand, you really have to understand the products of the genes and how they interact, which is more complex than just knowing the sequence of the genes.” –Clyde Hutchenson (1999)

p102 “Anticipation is the key to…biological survival and hence success… The anticipation we are talking about is deeper and more profound because it tunes in an organism to its broader environment. Francois Jacob, one of the great pioneers of molecular biology, said, “one of the deepest, one of the most general functions of living organisms is to look ahead, to produce a future.”


  • the VLPO (ventrolateral preoptic nucleus) of the anterior hypothalamus promotes sleep. Neurones from this nucleus release GABA (gamma-amino butyric acid), an inhibitory neurotransmitter of the nervous system. The neurones project to and inhibit the activity of the nuclei of the ascending arousal system, and the lateral hypothalamus (LH).
  • The ascending arousal system (AAS) of the brainstem and hypothalamus promotes wakefulness in the forebrain. Neurones from five regions in this complex (LDT, PPT, DR, LC, TMN) release several excitatory neurotransmiters. In the brainstem, neurones from teh LDT (laterodorsal tegmental nuclei) and PPT (pedunculopontine tegmental nuclei) project to the thalamus, and from there to the forebrain. These two nuclei are responsible for the release of acetylhoine. The LC (Locus coeruleus), also in the brainstem, has neurones that project the forebrain and release noradrenaline. the DR (dorsal raphe nucleus) of the brainstem has neurones that project to the forebrain and release serotonin In the hypothalamus, neurones from the TMN (tuberomammillary nucleus) project to the forebrain and release histamine.
  • The lateral hypothalamus also promotes wakefulness. Neurones from this nucleus release orexin (also called hypocretin), a very recently discovered neuropeptide. Neurones project to the nuclei of the ascending arousal system, the forebrain, as well as the VLPO.
  • The NREM/REM oscillator is a cluster of five separate nuclei in the brainstem that provides the switch between NREM and ReM sleep. Three of these nuclei, the LDT, PPT and BRF (brainstem reticular formation), are interconnected and excite the activity of both themselves and the two other nuclei involved in the NREM/REM oscillator. the LC and DR form a second functional unit. .The LC and DR are interconnected and inhibit the activity of both themselves and the LDT, PPT and BRF functional unit. This reciprocal set of interactions generatess a flip-flop switch that produces a roughly 90-minute oscillation in NREM and REM sleep.
  • The suprachiasmatic nuclei (SCN) regulate the various sleep structures of the brain either directly by neural or chemical outputs, or indirectly by teh release of the pineal hormone melatonin. Melatonin is high throughout the night, and when administered has been shown to increase the propensity for sleep in humans.

Rhythms in Humans





00:00-02:00 ↑sleep initiation

↓gastric motility


↑cerebral infarction

↑growth hormone

↑uric acid concentration

02:00-04:00 ↑gastric ulcer crises

↑gall bladder symptoms↑asthma



↑triacyl glycerol



04:00-06:00 ↓body temperature


↓deepest sleep

↓urine production


↑gastric ulcer crises









06:00-08:00 ↑sleepiness/tiredness ↑rheumatoid arthritis

↑allergic rhinitis







↑plasma catecholamines

↑fight or flight system

↑platelet viscosity

↑blood viscosity

↓fibrinolytic activity

↑NK-Cell activity

08:00-10:00 ↑bowel movement

↑blood pressure

↑heart rate

↑myocardial infarction


10:00-12:00 ↑concentration

↑Short-term memory

↑logical reasoning

↑blood pressure

↑myocardial infarction



12:00-14:00 ↑concentration

↑short-term memory

↑logical reasoning

↑urine production

↑airway patency

14:00-16:00 ↑insulin
16:00-18:00 ↑osteoarthritis


18:00-20:00 ↑body temperature


↑cardiovascular efficiency

↑muscle strength


↑grip strength

↓sleep propensity

20:00-22:00 ↑gastric acidity ↑skin sensitivity

↑menopausal flushes

303 Days to Dec 21st 2012