Saturday, September 24, 2016

Trees Look Serene, But Operate Under Very High Pressure

Xylem, phloem, turgor ... what the heck is going on in tall plants so they can drink from dizzying heights?

Atmospheric pressure is 76 cm of mercury, or 10.3 meters of water, or 0.1 MPa. That means that even a vacuum can't pull water up higher than 10 meters from the earth's surface. Yet Redwoods grow to 115 meters. How does that happen? There are two problems- where does the pulling force come from, and even with the requisite force, how can anything conduct water to far greater heights than a vacuum on bulk water would allow?

The answer to the second issue is capillary action. Plants have a circulatory system somewhat analogous to ours, with two parts going in opposite directions connected by tiny selective membranes. But there is no heart- no pump. Fluid is moved around by high pressure differentials, driven by osmotic differentials, strong cellular architecture, and active molecular transport at the sub-microscopic level.

One part (phloem, maybe analogous to arteries) is for the sugars produced by the leaves, called sap. The second is xylem, (maybe analogous to veins), conducting water and minerals up from the roots. Xylem is a dead, porous tissue inside the cambium. Using tiny, hydrophilic vessels allows water tension to "hold it all together", while the negative pressure at the top of a plant pulls continuously upwards. How much pressure is needed at the top of a plant? Well, about 19 atmospheres of negative pressure for a hundred-meter tall tree, or ~2MPa. (Compared to this, our blood pressure is negligible, at 0.015 MPa.) The xylem is carefully constructed to prevent bubbles from forming, and from spreading if they do form, helping the natural cohesion of water (which causes the phenomena of capillary action and surface tension) to keep the water column intact under such intense pressures.

Xylem, full of small conducting pores, and carefully isolated within the plant to sustain high negative pressures. The pores  also stand ready to break the spread of air, if any is introduced.


Just as interesting, however, is the phloem system, which generates high positive pressures and is integral to the whole circulatory regime. Phloem is living tissue- just outside the cambium (in trees) and specialized to conduct sugar fluid to sites that need it, like fruits and roots, all over the plant. The xylem and phloem systems are selectively interconnected. The key "capillary" point in the leaves where xylem fluid is drawn towards the phloem fluid, due to the osmotic pressure from a low-solute (xylem) to a high solute (sugary phloem) fluid, forms the pressure differential that makes the whole system work, by what is called the M√ľnch hypothesis.

It has taken decades to test this hypothesis, since it was proposed almost a century ago, for technical reasons- the second you cut into a plant to look at its phloem, the pressure drops in that region. A recent paper (review) used fluorescence tracers and microneedle probes as new methods to observe pressures and flow rates in living, whole plants- the morning glory vine.

Phloem, while largely empty space, has a complex internal surface, including walls (and companion cells) which contain the selective ionic barriers that keep sugars in while letting water and minerals from the xylem fluid enter, at least in locations like the leaves where that is useful. They also have open pores (sieve plate pores) between successive cells (called sieve tubes) that allow flow, but can quickly restrict it in case of injury. Sieve tubes even have their own type of plastid, whose function is entirely unknown.

Phloem sieve tube plates, aligned with a plant and locations from which they were sampled. The lower plates are more tilted to allow more flow. Their pores are also larger, though that is not so apparent here.

The morning glory vine was used for obvious reasons. It is highly accessible, easy to grow, grows to great heights, is easily manipulated, and has a thin stem that is easily dissected. In its stem, it has phloem both inside and outside of a xylem zone, which reinforces the idea that the xylem needs to be carefully protected from the atmosphere.

A stem section taken at four meters height. Phloem- dashed arrows, xylem- yellow and green arrows.

The researchers calculated the sap viscosity, its flow rate, and the phloem volume and cell structural characteristics, to come up with the pressures and other parameters required to achieve it. They also used micro-pressure guage needles and fluorescent dyes in the sap to attempt direct measurements on the phloem channels. Results where that the sap had a sugar concentration of 18%, and about 0.2MPa are needed per meter to drive sap flow. Over a seven meter plant, which was what they were studying at first, this amounts to about +1.4 MPa overall at the leaves, to drive fluid movement to the roots, which was indeed observed overall.

Next, they grew the plants to 17 meters high, removed the lower leaves to simplify the analysis, and measured again. The phloem pressure at the top was +2.2 MPa, which is high, but not enough by their prior analysis to get the fluid all the way to the roots. So they took a second look at the anatomy, and found that the plant had instituted structural changes to ease sap flow. The lower you are on the plant, the larger the pores between successive phloem cells, the larger and more tilted the pore plates themselves, and the higher the sap conductivity, up to six-fold. They conclude that the phloem system is pressure-driven, with the pressure carefully raised, along with other physiological parameters, to adapt to longer lengths of transport.

This leads to a unified picture of plant fluid transport, where very high pressures, both positive and negative, and clever anatomy, allow the transport of both key fluids- the water from the roots, and the precious photosythesized food from the leaves. Osmotic pressure is key at both ends, since not only does the high sugar content of the phloem sap drive root water towards it and supply its pressurization, but in the roots, a modest level of sugar and/or other concentrated ions drives water from the surrounding soils into the root, the pressure of which varies in different plants.



  • Another evil lobby & product, in the grand tradition of guns, tobacco and oil: sugar.
  • The banks are worse, not better.
  • Indeed, our economy is ridden with bigger and more entrenched companies than ever.
  • Why do we keep paying for this moral travesty?
  • Equality- do we want it or not?
  • Actually, the Fed should cut rates.
  • Insurrection, treason, and terrorism has its partisans, and a loving US memorial.
  • A race to the bottom, in Tennessee.
  • A gene involved in the folding of hominid brains.
  • When Obama pulled the veil of colorblindness. There was a black America and a white America, after all.
  • A key tool to address inequality: the estate tax. Guess what the Trump position is?

Saturday, September 17, 2016

The Desktop is Dead

Stick computers like the Chromebit are part of our future- tiny, portable, cheap.

As someone who consults frequently on personal computer issues, it was interesting to hear about a new form factor- the stick computer. The leading example is the Chromebit. Chrome books are better known- petite laptops that give you a Google Chrome browser that is a portal to the whole web, including a series of web apps and soon, android apps as well. The Chromecast product is also better known, as a tiny computer that lets you channel WiFi streams into your TV, using a phone as a remote controller.



The Chromebit is a bit of each, with a small size of the Chromecast, a bargain basement price of $85, and the computer capabilities of a Chrome computer. Like the Chromecast, it plugs into an HDMI port on any TV or monitor. But it turns that screen into a computer, given that web apps such as mail, docs, and storage now allow one to work entirely online, including cloud printing. Storage is negligible, so everything has to go to Google drive or some similar online service. Likewise, connectivity is minimal, with one USB 2.0 port- enough for connecting a camera in a pinch, or a keyboard or mouse, though these should be bluetooth. Naturally, you have to be online to do anything with this device.


Intel and Android also offer stick computers. At $150, the Intel stick is a fully stocked Windows 10 computer, though with only 32G of storage. Android sticks do not offer full computer capability, being restricted to apps, like a tablet, but these capabilities obviously run quite a gamut, from skype to web browsing, voice control, and millions of other programs.

For a person on a tight budget, these computers are an impressive way to get online with minimal expense, and one can use an existing TV to save even more. A full system would run something like...

$85 - computer
$15 - bluetooth mouse
$30 - bluetooth keyboard
$70 - cloud-compatible printer (optional)
$100- monitor with HDMI (or use existing TV)
=====
$300

This is impressive from a budget perspective, but it also indicates something about the future. One can imagine a world where our phones act as the computers behind everthing we do, which we can plug into dumb screens wherever we want, turing them into secure, full computers. Whether the applications also reside in the cloud as Google is working towards, reducing reliance on any local computing power, is uncertain. This depends only on slightly faster network connections than most of us have today to make fully animated clients driven almost entirely from distant sources. How much we can trust those corporate, centralized sources in an always-connected ecosystem to serve us faithfully is, naturally, another question.



Meanwhile, while we are on tech issues, to power all these bluetooth devices, rechargeable batteries are the sustainable and cost-effective solution. Charging such batteries can be tricky. It pays to use a smart charger that operates not just on a timer as most chargers do, but by sensing the status of the battery.


  • Gerrymandering has brought us a crazy, unrepresentative House. There ought to be a law, right?
  • Both retrograde forces in the Arab world have more power (and arms) than the progressives.
  • Crime pays.
  • It's not easy being the only super-power.
  • Republicans fight in the gutter. Then they call others "crooked".
  • A lesson in psychological projection.
  • Bill Moyers and the Housewive's Rebellion.
  • People with a modicum of compassion, vs Trump.
  • What's going on in Puerto Rico?
  • Over a 1 million-mile lifetime on the roads, you have a 1 in 90 risk of dying in a crash. That is not good enough.
  • Annals of waste, pork, and fraud.
  • Health care markets still don't work very well.
  • Recidivism from Guantanamo.

Saturday, September 10, 2016

Association, Attention, and Gamma Waves

Associative memory gets broken down by frequency band and location.

Do you have your own madelaine? A place, song, taste, or feel that transports you into the past? That is associative memory, retrieving a more complete set of experiences based on a relatively simple, (if uncannily specific) cue. It may seem effortless, but under the hood, a great deal is obviously going on. Memory is associated with the hippocampus structure deep within the brain. Missing that structure blocks formation of new memories or retrieval memories by association. (Though some older memories may still be available- it is not clear yet whether memories are stored exclusively in the hippocampus, or are only staged there for eventual transfer to other parts of the cortex for long-term storage.)
"Specifically, dense recurrent connections among CA3 pyramidal cells [in the hippocampus] are thought to allow, after a single exposure, for auto-associative reinstatement of a previous learning pattern upon receiving a retrieval cue. Consistent with a role for pattern completion, selective knock-out of the CA3 NMDA receptor was shown to result in impaired memory on a Morris water maze when only partial environmental cues were available, i.e. when performance presumably relied more strongly on successful pattern completion."

A recent paper makes use of direct recording in the brains of surgical patients to observe neural activity and rhythyms as they learn and recall events. Given enough analysis, one can "fingerprint" particular experiences, and see that they are represented similarly when they first occur, and again when they are remembered. The acuity of being able to put electrodes directly into the hippocampus is far higher than the non-invasive methods of fMRI.

The test was to present patients with words and pictures to make an association. Then later, the word alone was presented and the patient asked to remember the full scene. Or a control word with no association was presented. The latter was called item recognition, which involves others types of recall, while the former was called associative recognition.

Correlation between the first presentation and the recall event, in activity from the hippocampus electrodes. For associative recall, (vs item recall) the correlation is clearly higher and more complex. The AR surrogate data comes from the average of the original readings during the presentation of the AR stimulus/scenes, rather than their recall, as an additional control similar to the item recall.
It is clear that associative recall generates a richer experience and richer readings from the hippocampus. That is not news, really. What was interesting was that the researchers had access to far more activity detail and could especially look at the rhythmic effects of this recall.

A dramatic increase in gamma waves as recall happens. Concurrently, alpha waves decline.

That is basically it for this rather short paper. They make the key points that recall involves re-representation of the original stimulus, in some form that is detected by these electrode readings, though far from being understood or decoded by them. And secondly that this recall is accompanied, on this very local basis, by a big increase in gamma wave activity and a decrease in alpha wave activity. This all agrees with the developing paradigm, which is that alpha wave patterns correlate with default / resting brain activity, while gamma waves happen during attention and intense thought. Gamma waves are not carriers of information the way radio waves are, but seem to represent the coordination of select areas of the brain as they form ad-hoc coalitions to attend to some thing- the spotlight of attention, and of consciousness.



  • Capitalism is going to the dogs.
  • And ends up sabotaging our infrastructure and lives, if there's a profit.
  • A philosophy and culture of non-accountability.
  • Yes, a right-wing conspiracy. And love of innuendo.
  • Trump puts it out there for all to see.
  • But who is really paying attention?
  • Certainly not his own party.
  • Please, please don't pay us any taxes!
  • Good thing she's not governor.
  • Climate apathy is bad too.
  • Sometimes, math is just a curtain to hide intuition and bias.
  • Gazprom: corruption, bloat, and decline.

Saturday, September 3, 2016

Living on the Spectrum

Of sexuality, and other existential dimensions.

It is common now to refer to people diagnosed with autism as being "on the spectrum". The disorder is unusual for the number of genes whose mutation can contribute to it, estimated at about 100 to 400. Thus it is easy to see why affected people turn up with a wide spectrum of phenotypes, and indeed why that spectrum extends well into the "normal" range- people who may be only slightly odd, but never formally diagnosed.

But we live on many other spectra of talent, capability, being. Indeed everything about us is variable. Height, color, sociability, musical ability, extraversion, intelligence are common examples. A recent story in the New Yorker profiled a London police unit of specialists who recognize faces. It turns out that people occupy a wide spectrum of facial recognition talent, from those who can not recognize themselves in a mirror, to those who never forget a face, no matter how briefly glimpsed. It is a capability that is so private and obscure that people typically do not realize what the normal range is and where they fall in its spectrum. So it is only with the burgeoning video surveillance carried out in Britain that high levels of this talent became belatedly recognized as relatively common as well as useful.

One of the most interesting spectra is that of gender. The Olympics reminded us (among many other forms of diversity) that diversity among humans extends to a spectrum of gender. Indeed, one's biological gender, and the gender one feels oneself to be, and the gender one is sexually attracted to, each seem to lie on spectra that, while usually correlated with the "normal" axes and occupying a bimodal distribution, can range spectacularly, and independently, to far reaches.

This is particularly interesting in light of the tight and binary social construction that has traditionally been put on gender. Why is that? Why enforce uniformity where there is variability? An interesting book about the philosophy of the Matrix series of films poses a similar question, in the context of Zion, which tries to be a gender-neutral society, as opposed to the Matrix, which is conventionally normed. Can we escape binary thinking? Should we?

I can think of three general hypotheses. First is pure patriarchy and power. The clear delineation of gender, as also happens in white/black racism with the one-drop rule, eliminates ambiguity when power is being divided up, with all power going to one group, and not the other. Oppression is much harder to institutionalize (and tribalize) without simple rules about who is in, and who is out. Setting the "normal" standard for each class is also a form of social power, as everyone in junior high school learns. When power and attractiveness are properties by definition of the "typical" and "normal", the social system maintains itself in a consistent, conservative way.


A second reason is simply our way of thinking. We are habitually reductionistic, thinking in cartoons and schematics. Cars are reduced to metaphorical "wheels", men and women are objectified mutually to their most basic aspects and organs. With a natural bimodal distribution of gender, it is natural to schematize them as two clear classes, declare those as "normal" and then be made uncomfortable by deviation from that simple mental model. Perhaps, conceptually, humans do not "do" diversity terribly well, since our understanding of the world depends so strongly on our capacity to make "sense", i.e. rules and schemata, out of the welter of reality.

Thirdly, one might turn to deeper psychology, seeing that our models for existence come from complex, unconscious archetypes. The mother/female and father/male archetypes are probably the most powerful we have. Whole religions have been founded on each, with the father especially blowing up to cosmic, infinite, and omnipotent proportions. Conversely, the Catholic church has a difficult time controlling the growth of the mother archetype in the person of the Madonna, which in some regions such as Mexico can even put Jesus in the shade.

So we have to fight on numerious psychological fronts to deal with reality in an honest way, especially to interact with the reality and psychology of others fairly.