BASICS: "Hummingbirds.....where is the person, I ask, who, on observing this glittering fragment of the rainbow, would not pause, admire, and turn his mind with reverence..." (J. J. Audubon).
This is a blog about my summer life at the Baiting Hollow Hummingbird Sanctuary, at my winter garden, Calypso, in the Bahamas, and aspects of life in general.
This private sanctuary is now permanently closed to the general public, as a result of a lawsuit brought by a neighbor. Only my friends and personal guests may visit (

Thursday, May 29, 2014

Reggie retiring; I will represent myself

I mentioned in my last post that there had been another important development in the lawsuit against me, which seeks to close down the sanctuary, and also $3 million in damages. Shortly before I left Eleuthera, my lawyer Regina Seltzer informed me that she would be retiring and would not be able to represent me beyond the may 27 Preliminary Conference, although she would continue to offer legal advice and assistance. I have delayed announcing this because I wanted to fully reflect on the implications. Reggie has performed wonderful work for me (and so many others in the past) and it has been a pleasure and honor to get to know her. She prepared an initial formal Answer to this ridiculous suit, laying out grounds for an effective defense. She has guided me through the subsequent process, including the abortive "PC" and the paperwork required to notify the change in representation. I have decided, after careful reflection, some soul searching, and consulting other lawyers, to represent myself,  acting "pro se" as the jargon goes. A ton more jargon and paperwork ahead, and additional stress, and in many ways a complete waste of time and energy that could be poured instead into science and teaching.

But while I still have important science left in me, I have to recognize that my best work there is probably behind me, and that I should rise to the presented occasion. I have an opportunity now to contribute to society in a different way: to throw some light on a sometimes rather sleazy area of public life from which so far I've been mercifully insulated: the law and its practitioners, local government, the press etc etc, and of course to fight for a small chip of natural beauty literally in my own backyard. Of course not all lawyers and politicians are bad apples, and I look forward to meeting the better ones. For a penetrating analysis of rot at even the loftiest levels of the legal system, see Linda Greenhouse's excellent article about the Supreme Court in today's NY Times (

I feel I understand the main points of law involved, and am capable of grasping most of the rather arcane procedures involved. Hopefully I will discover that these laws and procedures have evolved based on a core of fairness and efficiency, and not just to line lawyers' pockets, as it at first seems.

The lawsuit revolves around a petty dispute between a handful of neighbors, but it also raises important issues about the legality of backyard birding (one of America's most popular outdoor activities), and I hope that it will throw some light on needed changes in the way New York handles pro-se defendants and court procedures generally. In some ways scientists and lawyers do the same thing: they are highly trained professionals who deal in evidence and logical analysis and argument. Facts and theories about them. Of course their criteria are somewhat different: truth versus money; understanding versus power; generality versus particularity. However, each profession can perhaps learn something from the other.

Reggie was initially enthusiastic about my representing myself, but changed her mind after Tohill's (= plaintiffs' lawyer)  behavior at the PC. She fears I am a lamb going to the slaughter. Perhaps, but the slaughter is likely going to be prolonged, public and revelatory. But possibly even at this late hour the plaintiffs will agree to a direct negotiation to attempt to resolve our dispute, with compromise on both sides.

The picture is from last year, by Jeevenan Gopikrishna, and shows the willowy bloom of bog sage, Salvia uliginosa (I'm planting lots of these right at this moment).

Tuesday, May 27, 2014

Lawsuit "Preliminary Conference" report

Together with my lawyer Reggie Seltzer I attended the Preliminary Conference ("PC") in the lawsuit "Terry v. Adams", at the Riverhead Supreme Court (where my close neighbor and principal complainant is a Judge). The building was swarming with suited and cravated lawyers. At my wife's urging I wore a clean white shirt and sports jacket, but no tie (garotting is not allowed in a civil lawsuit). I also throughly cleaned my fingernails, which were black after 2 days of dirt-gardening. The meeting was held in a large room with a dozen large tables. I arrived before the others and, after showing my papers, was directed to choose a table. Since there was at least one person already at every table, I chose a table with only one other person, clearly another lawyer who was studying his papers, presumably in relation to another case. After a few minutes Reggie arrived, and somewhat after the appointed time (10 am) 2 other gentleman showed up. First a young man with a name I did not recognize. It turned out he was an associate lawyer with the firm appointed by my son's umbrella insurance company, which apparently covers him in this sort of case. Of course I don't have any form of insurance on the Baiting Hollow property, and our insurance on our home in Stony Brook is not of the umbrella type. A bit later Mr Tohill arrived, who I was obviously interested to see, for the first time.

The room was very noisy, and of course I very recently went deaf in both ears (probably seawater in the middle ears).  On arriving back in the US I had ordered a new type of inexpensive Bluetooth-based  hearing aid (which had received excellent recent reviews in the NY Times (see, from a company called Sound World Solutions. Basically it works quite well and helps me with understanding normal   speaking, but it amplifies all sorts of distracting noises, so the room sounded like bedlam. I'll write more about this in a future post.

Reggie raised a couple of the issues we had discussed at our meeting on friday, including the possibility of a direct negotiation between the parties instead of continuing with the lawsuit (and another complicating issue I will write about separately).  Tohill seemed to become enraged, brusquely saying that it was most improper not to have notified him about these developments prior to the PC, and abruptly demanding, and apparently obtaining (without our participation or agreement), an adjournment (to, apparently, june 18) , and immediately departing in a huff.  Since I only returned to the US on may 21, and only met, for the first time, with Reggie on may 23, and since the following 3 days were holidays, it hardly seemed practical to inform him, in writing or even by phone, prior to our early tuesday scheduled meeting. Furthermore, it's my understanding that the sort of issues we were attempting to raise are indeed appropriate to a PC (see, and specifically:

"More than simply setting deadlines for discovery, at a preliminary conference, litigants are expected to consider and be prepared to discuss:
  • the simplification of factual and legal issues, where appropriate;
  • the addition of other necessary parties;
  • settlement of the action;
  • removal to a lower court pursuant to CPLR 325(d), if appropriate; and
  • any other matters that the court may deem relevant.
I felt that Tohill treated Regina (who is a very distinguished and gentle lady in her eighties)  and I with contempt. These issues should have been discussed at the meeting, and then the meeting could have been adjourned.

We have now decided to submit a "Motion to Dismiss", based particularly on our impression of Tohill's ruthlessness, as well as the extreme weakness of their complaint. This Motion would further postpone the adjourned PC.  But if this, or the proposed direct negotiation, fails I shall enjoy vanquishing him utterly.

Sorry the news is bad and only partial - there's a lot more to say and digest but this will do for now. In the meantime enjoy the above stills of pink ladyslippers and columbine both in bloom now at the sanctuary.

Monday, May 26, 2014

yesterday at the sanctuary

Mostly just hard work, but during short breaks I did see quite a bit of activity, with both males and females making brief visits to various feeders. Then, in the evening, while eating supper on the back deck, I saw a male ("The" male?) first visit a feeder just in front of me, then come and perch for 30 seconds on a twig on the back deck no more than 10 feet away. He looked rather handsome. Then, he went quickly in succession to 3 more feeders around the back deck. he was clearly checking that they had good nectar, and should be included in his patrols of his territory. I've added some feeders along the  Woodland Walk, and I'll watch to see if he has also added those to his patrol. A few minutes later he re-appeared and launched a mating dance almost over my head. Not super-high (15 feet?) and onlyabout a half dozen swings. The recipient of his attentions appeared to be in a Viburnum carlesii bush just in front of the deck, but she was obsured from my view by leaves.
I suspect I'm seeing the settling in of resident hummers, and that activity will dwindle as the females start nesting.

As I wrote before my camera has packed in ("System Error Zoom"), so I'm posting a couple of videos from 2 days ago. The first shows a hummer briefly hovering over a clump of native columbine (Aquilegia condenses), the main hummer-flower at this time of year (though the coral honeysuckle blossoms are opening up too).

The second video shows some flowering iris (not a hummer-plant) and columbine

Friday, May 23, 2014

First Report from the sanctuary

I arrived at the sanctuary yesterday afternoon. Lots to do over the next few weeks, but within a few minutes of sitting down outside for a post-lunch espresso, I saw an adult male hummingbird briefly visiting a clump of native columbine (Aquilegia canadensis). The feeders were all empty, but were quickly refilled and extended. No further sightings until midday today, when I saw him at a feeder for a couple of seconds only.
Brief rare sightings like this are common at the start of the season: the male spends little time feeding at one spot and is mostly doing the rounds of his territory.
The coral honeysuckle is starting to bloom, and though not for hummers so are the pink ladyslippers and some iris, and 2 brave wild dogwoods The variations on fresh green on the trees in the western valley are breathtaking. But it's so cold, wet and gray, especially after Eleuthera. Brrrr! Although there was a blissful hour of dim sun late this afternoon.
This morning I met with my lawyer Reggie Seltzer to discuss lawsuit tactics for the Preliminary Conference on tuesday morning. Unfortunately snorkeling in Eleuthera has waterlogged both my middle ears, and for 2 weeks now I've been almost deaf (except, infuriatingly, to the sound of my own mastication). Only the helicopters on their way to East Hampton for the long weekend break the silence.
On with the mowing, weeding, planting, and repairs after the hard winter. Very few of my half-hardy hummer-favorite salvias came through the cold, so will have to start again from scratch.
But despite everything it's good to be back - another world, but beautiful too, which I look forward to sharing with you via this blog, and, in august, in person.

Wednesday, May 21, 2014

On our way; Calypso flowers

The top image is a pink hibiscus and the bottom shows frangipani in the foreground, with firecracker, bougainvillea, oleander and an orange bromeliad. Many frangipani flowers of various colors were in flower as we leave the island. The white frangipani is the most fragrant (see below), indeed it's perhaps my favorite perfume, even more so than gardenia.

We are waiting for our 9.20 Bahamas Air flight to Nassau here at the seaside little airport of Governor's Harbour, Eleuthera (which has free internet!). They say "If you have time to spare, fly Bahamas Air", so I hope it's not too late to reach Nassau in good time for our 1.10 pm Jetblue flight to JFK. The flight time to Nassau is only 15 minutes!

In the past we always used to fly direct to Fort Lauderdale. However, direct GHB-FLL flights have become almost extinct. For many years we used to fly Twin Air, out of the private Jet Center at FLL. We always felt that our winter residency started when we arrived at the Jet Center, usually in time for a leasurely lunch at the Aviator's Cafe, before our quick (1hour) flight to Eleuthera. However, the wonderful Twin Air's planes slowly disintegrated (occasionally midair) and finally the operation collapsed.

We always used to drive slowly from NY to Lauderdale, taking a whole week and visiting many of the historic places on the east coast, starting just south of Washington. Some of our favorite places: James River plantations, Edenton and Wilmington NC (where our middle son lives), Charleston, Beaufort, Savannah, Shellman Bluff, Darien, St Augustine, but there are many other charming out of the way spots as well. Perhaps I'' feature a few of these in future posts.

I hope the shock of the quick return to NY, rather than our former slow adaptation. will not be too great.

Tuesday, May 20, 2014

au revoir Eleuthera; Bahama Woodstar male hummingbird

Here's a short clip of an adult male Bahama Woodstar hummingbird, just outside our bedroom window. He's perched on a twig of a large Night-Blooming Jasmine (not in flower at the moment) which has, at night, an almost overpoweringly sweet fragrance. Note the purple throat (only visible from certain angles). He's guarding a very large clump of firecracker flowers (Russellia equisetiformis) which is next to outdoor shower area. Is this Gumbo's mate?
All being well we return to Long Island tomorrow, and I will be reporting soon from the Baiting Hollow Hummingbird Sanctuary.

Thursday, May 15, 2014

Pick Up your hummingbird plants this weekend in Medford!

The photo was taken at the BH Sanctuary last year by Rick Mei. The hummer is feeding at cardinal flower, a superb hummer-friendly perennial for Long Island.

The best place to get hummingbird plants on Long Island is at a surprisingly secluded spot in Medford, not far from the LIE. They have a new website and will be open this weekend. I predict they will be quickly sold out.

Please bear in mind that the Baiting Hollow Hummingbird Sanctuary is CLOSED until august. Please see these pages for updates.

Wednesday, May 14, 2014

Preliminary Conference scheduled for lawsuit; imperfect synapses cannot learn

A "Preliminary Conference" has been scheduled for may 21 in the lawsuit brought against me and my son Rafael, which seeks to close the Baiting Hollow Hummingbird Sanctuary, and also demands $3 million in damages. I believe this conference, which I plan to attend, will establish a general timetable for "discovery" by the 2 sides, i.e. the process by which the plaintiffs (the Terrys, the Bherwanis and Ms Hamilton) and the defendants (Paul and Rafael Adams) will seek relevant information (such as website content, emails and other types of exchange). In particular I anticipate that all the parties to the lawsuit, plus some additional parties, will have to make depositions (i.e. formal recorded answers to specific questions posed by one side or the other). The aim of this "Discovery" process is to establish a set of basic facts which all parties can agree on; this would reveal whether the lawsuit has any merit, and what results a trial might lead to, in which case the parties could attempt to settle matters before trial.

Obviously I'm going to have to invest a considerable amount of time and effort into learning about arcane legal procedures. Hopefully I will discover that these procedures are mostly sensible and effective, and designed to efficiently establish true facts and reasonable conclusions, rather than line lawyers' pockets.

It's also possible that the possibility of "mediation" could be raised at this conference. This would involve all parties agreeing to abide by the decisions of an unbiassed external mediator. I've heard rumors that the main requirements of the plaintiffs in such a mediation might be changing the name from "sanctuary" (apparently this name, meant to denote peace, natural preservation and tranquillity, is particularly offensive), and compelling all my visitors to park down near Sound Avenue (eg at the Sound Ave Preserve parking lot) and walk up Terry Farm Road. I would be interested to hear my readers' comments on these issues.

OK, back to science. My colleagues (Kingsley Cox and Anca Radulescu) and I have constructed computer models of networks of "toy" neurons which can learn using Hebbian imperfect synapses.
There are 2 key parts to these models. First and simplest is a way to generate data that can drive learning. One way would be to use a movie, each frame of which is a set of numbers (i.e. pixels). Or one could just use a sequence of "natural" images (e.g. photos of natural scenes, in no particular order. The problem with this is that one does not know what one is supposed to learn from such images - one doesn't really know how they were generated (at least explicitly - of course one might know who directed and filmed the movie etc). And these data are far too complex.

So instead we generate the input data in a completely well-defined way. For example, we can start with a set of random numbers. They are random in 2 senses (1) each number in the set is independently chosen: knowing one number tells one nothing about another (2) they all follow some simple statistical distribution (random means that it can take a range of possible values, each with a defined probability, which constitutes its "distribution". The Gaussian, or bell-shaped distribution is the most familiar example. These random numbers are not directly used as the input: in fact, since they are independent and random, they are completely unstructured - there would be nothing to learn, just as the snowflakes on an old fashioned TV after the channel shuts down are not meaningful. We introduce structure by mixing these random numbers together in a defined way, to generate a new set of numbers. For example, the first number in the new set is created by taking a fixed fraction of the first number in the original, random and independent set, and adding another fixed fraction of the second number in the original set, and so on for all the numbers in the original set.

Tuesday, May 13, 2014

Hummingbird WebCam

Lanny Chambers has an excellent website about hummingbirds, and his brother maintains a wonderful WebCam showing ruby throated hummers visiting his yard on Catoctin Mountain, Maryland (near Camp David). At the moment nesting is in progress and there is rather little activity, but it will become very busy later in the season.

In the meantime, here's another photo of the hummer currently visiting Melissa Hahn's yard on the north shore of Long Island.

Let's resume our peek under the hood of the brain. In my last post I wrote about the crucial importance of Hebbian synapses. Each cortical neuron receives thousands of these synapses from its input cells, and in turn makes thousands of synapses on its targets. The strength of a synapse determines how much signal each input contributes to the overall output of a neuron. The strength of a synapse is in turn regulated by the sizes of the signals that reach it - the input ("presynaptic") and output ("postsynaptic") signals.  Of course this creates something of a vicious circle: the stronger a synapse, the more that input contributes to the output, tending to further strengthen the synapse. But as long as some mechanism prevents all the synapses, or the overall output, from becoming too strong, this "Hebbian" rule leads to selective growth of some synapses at the expense of others, in a way that reflects the overall correlation structure of the input stream.

Ideally what one wants is for particular neurons to adjust their synaptic "recipe" so that the output of a neuron tends to track not the original sensory data, but one of the underlying "causes" of that data. The idea here is that what we literally see (eg a particular set of pixel intensities) reflects the occurence of certain objects in front of us - perhaps a cup, or a hand, or both. If there's a "cup" neuron which fires whenever there's a cup it could be very useful, because it could be used to trigger a particular action (e.g. drinking). But because the particular sets of pixel levels triggered by all possible images of cups is extremely variable, and overlapping those triggered by hands, it's not possible to immediately build a "cup" neuron. It has to be done gradually, in many levels, by gradually assembly more promitive features (lines, curves, handles etc). Hebbian synapses can slowly build such networks of cause-detecting neurons. Of course what we are doing when we "understand" something is successfully identify the causal structure, or "meaning", of our immediate or our past experience. For example, we gradually learn how to recognize and use a completely unfamiliar object, or even a scientific or legal concept.

Does the brain have  Hebbian synapses and how do they actually work? Recent research has revealed that almost all synapses are Hebbian. The synapse contains specialized intricate machinery that allows it to measure the voltages of both input and output neurons and adjust the synapse strength accordingly. If the synapse fails to strengthen over a long period of time, it is removed, and other new ones, from alternative inputs,  are created. Describing this fascinating machinery would take too long, but there is a master chemical, ionized calcium, that acts as the key signal that both input and output voltages are strong, and that ultimately triggers strengthening.

With this background, we can finally look directly at my own scientific research. I am interested in a simple, rather obvious, but previously unaddressed question. Given that Hebbian synapses exist and play a central role in learning to understand the world, how accurate must they be? In particular, because there are a quadrillion of them, it must be quite difficult for the brain to ensure that the right ones get tweaked at the right time: the needle in a billion haystacks problem. At first glance the Hebbian rule seems to solve this problem: each synapse has to follow the Hebb rule, and adjusts its own strength according to its own unique past history of coupled input and output voltages, WITHOUT AFFECTING THE STRENGTH OF ANY OF THE OTHER QUADRiLLION SYNAPSES.

The problem is that as synapses, as well as being Hebbian (individually adjusting their strength according to the past history of their conjoint pre- and post-synaptic voltages) must also do something else: they must rapidly communicate the signal of the presynaptic axon to the postsynaptic neuron. What this means is that synapses have to do 2 contradictory things: communicate and be independent, spread and stick, be coupled and be isolated. My co-workers and I hypothesized that real biological Hebb synapses (unlike those of theorists, modellers, and artificial intelligence experts) might not be able to accomplush these 2 contradictory tasks perfectly. In concrete terms, we think that the calcium master signal which tells a synapse to strengthen might very occasionly leak out of a synapse and affect some of the neighboring synapses. Indeed, there is some, rather controversial, evidence that this can happen.

What this means is that the grand speculation I outlined about Hebbian synapses leading automatically to networks of intelligent neurons might collapse in practice. This would mean that a century of neuroscience "advances" would have been on the wrong track, and that something else must be going on in the brain (dancing flames? tiny ghosts? quantum microtubules?).

We set out to test this possibility, and see if the available theoretical models of self-organizing neural networks that can exhibit intelligent behavior (and that have recently started to achieve practical success, e.g. "Siri", "Watson", self-driving cars etc) would indeed collapse if their synapses were even very slightly imperfect.

To do this we made a simple computer model of a Hebbian neural network learning to extract "causes" from "observations". We modeled the simplest possible situation, a single neuron learning to extract a single cause from a series of input data. This model is far simpler than those needed to learn how to recognize objects, but we reasoned that if even the simplest most robust models cannot work as advertised, more realistic and complicated models would be unlikely to do better. I'll describe this in more detail in the next post. I'll also let you know about a new development in the lawsuit saga.

Monday, May 12, 2014

Hebbian synapses

I described in the last post how a neuron combines the signals from other neurons via connections called synapses, and sends the result, after some additional simple manipulation (analogous to "cooking") to neurons at the next level. These signals are small electrical voltages, sent over wires called "axons". When an axon reaches the vicinity of its potential target neurons, it starts to branch profusely, in 3 dimensions. These terminal branches may occupy a volume of several cubic millimeters. The target neurons also branch extensively, forming structures called dendrites. Wherever the axon branches of one neuron and the dendritic branches of another neuron happen to pass very close to each other (within a thousandth of a millimeter), a synapse can form between them. The synapse is formed as a result of a tiny fingerlike protrusion from a dendrite, called a "spine". There could be tens of thousands of target neurons within range of a given axon, though not every possible connection is permanently made - only those connections which work well survive.

The crucial issue is, which synaptic connections become permanent, and what is the strength of those synapses? This determines the special "recipe" that the neuron uses to combine the tens of thousands of possible ingredients. One possibility is that the recipe is set by a master "cook-book", which would be basically the genes of the individual to whose brain the neuron belongs. Indeed it seems likely that in many simple organisms such as worms and flies this is a major part of the process. Evolution, over millions of years, has learned what recipes work for this particular individual, regardless of personal experience, and the brain slavishly follows this standard recipe.

But the cortex seems to be much more flexible: it uses the experience of the individual rather than that of the species. This does NOT mean that each brain has an inner "genie" who records the experiences of the individual, flitting around adjusting the strengths of the trillions of individual connections. Neuroscientists believe there is no inner "genie", no "Ghost in the Machine". Indeed an individual synapse does not have access to the "experiences of the individual". What it does have access to, almost by definition, is the voltages in both the input neuron (the axon side of the synapse) and the output neuron (the dendrite side of the synapse). Typically the synapse multiplies these voltages together, and, depending on whether the result is negative, positive or close to zero, slightly decreases, increases or leaves unchanged the strength of the synapse. Remember that the current strength of the synapse determines the amount of the specific ingredient (in this case, this particular axon) contributes to the neuron's recipe.

This simple rule is known as "Hebbian learning", in honor of the canadian psychologist Donald Hebb, who first clearly proposed it. It's often summarized, rather crudely, as "Neurons that Fire Together, Wire Together".  This is the crux of the matter: thoughts are just firings of neurons, and the pattern of firings (and hence the thought) is set by the strengths of synapses, which are set in turn by the previous firings of neurons! While this might seem an absurdly trivial basis for the glories and squalors of the human mind, the fact that it's going on every thousandth of a second over one's whole lifetime, and happening at each of the quadrillion synapses (for the cognoscenti that's 10^12 X 10^15 = 10^27 or about Avogadros's number).

More to the point, it works. The reason why it works is as follows. The cortex is looking for the hidden structure in the ceaseless flow of one's experiences - this is what allows it to identify a cup as a cup. These experiences are really just vast arrays of numbers, pouring into the brain as an Amazon of data. But while these numbers almost look random, they exhibit subtle but strong structure, or "correlations".
(remember that if x and y both vary, and y tends to increase when x increases, they are positively correlated).

The Hebb rule is basically a correlation detector: it wires up 2 cells (input and output) if they fire together. In particular, since the overall output of a neuron depends (by definition) on what all the inputs are doing, then if a synapse is strengthened by the correlation between input and output, it is strengthened as a result of correlations between its various inputs. What this means is that a neuron can discover the hidden structure behind the apparently random flux of its ever-changing inputs: it can discover the meaning of the information it receives. In principle it can signal when a unique particular pattern of inputs occurs.

Well, I realize this is tough-going for the average hummingbird-lover! And there's a lot more to cover. But we got over the worst, and most important, bit: the idea of the "Hebbian Synapse".

To end up, let's me give you an analogy - a very useful and powerful one. The immense diversity and magnificence of life, ranging from the hummingbird to the tiger, and the jellyfish to the Royal Palm, is at bottom built on a very simple "trivial" rule, known as Crick-Watson base pairing. You should vaguely remember it: A goes with T and C goes with G (these are the building blocks of genes). There's now absolutely no question that the repeated application of this silly little rule over the whole earth over the last 4 billion years has generated hummingbirds, tigers, Royal Palms and us. It's much less certain that the mind is the result of the repeated application, over a lifetime and a quadrillion synapses, of the Hebb Rule. But I would bet a considerable sum (and my scientific career) that it is. And I don't find either of these conclusions depressing - indeed, as we will see, they amount to miracles.

Sunday, May 11, 2014

2 males at war; brainy brains

Back on april 15 I reported the early arrival of a male ruby throated hummingbird on the North Shore of Long Island, not very far from the Baiting Hollow Hummingbird Sanctuary. This male settled in, but now a second male is also claiming this yard as his territory. It will be interesting to see how they settle this: will one take over the whole place, or will they agree to split the goodies (an excellent hummer-friendly yard full of flower and feeders, and hopefully a bevy of visiting females)? More to follow. But here's a recent photo.

Continuing our short journey into the brain, we saw how the neocortex is divided up into specialized areas, with information sent from one to the next, and gradually distilled down to ideas, thoughts, plans, concepts etc. But how is the information sent and, most important, how is it transformed? For example, how does the cortex figure out that what one currently sees (basically the snapshot of the world provided by the eyes, a vast array of pixels like the output of a digital camera) is a cup, a hand, a computer screen or a hummingbird (and sometimes several of these at once?) This blog has hundreds of snapshots of hummingbirds - what do they all have in common? One might suppose they all have particular shapes, colors and textures - for example a red throat surmounted by a green head with a long narrow protruding beak. But what exactly does a "head" look like, or a throat, or a beak? And if the head is made up of eyes, ears, and sometimes feathers, what exactly are all these? Can one say that a particular set of pixels (basically, just an array of numbers) is a head?

The general idea is that things are made of parts, which are in turn made of other parts, and so on, until one gets to "parts" that are made of certain arrangements of pixels, in a hierarchy. Parts at the bottom of the hierarchy might be extremely simple shapes such as lines, or blobs, or wiggles. At each level of the hierachy, the "parts" would be represented by numbers - rather obviously so in the case of pixels. Thus an image could be described as an array of pixels at the bottom of the hierarchy, but also as a set of oriented short lines at various positions at the next level, and so on. At each level the number currently associated with each part is represented as a voltage across the membrane of neuron (or as a frequency or "firing rate") - like AM or AM radio. Neuroscience knows a lot about how these electrical signals are generated.

But the crucial step is moving from one level to the next: all the neuronal voltages at one level (e.g. representing pixels) have to be converted to new sets of neuronal voltage (eg representing oriented lines) at the next level. This is done because each neuron at one level contributes a little bit of its voltage to each neuron at the next level: a neuron at level 2 combines the voltages from many neurons at level 1 (but far from all), to varying degrees, depending on the strength of the connections from level 1 to level 2. The pixel to line transformation requires very specific connections between the 2 levels, each with its own particular strength, or "weight".

Now if one simply followed this recipe from level to level, one might as well go straight from the first level (the eye) to the last (the level that decides what one is seeing), combining all the mixing done at each level into a final blend, rather as when making a cocktail just adding in all the ingredients at random, without paying attention to their order. But in fact the order is vital, which means that a neuron must nonlinearly transform its weighted incoming signals before sending them to the next level.

The overall recipe for each neuron is, take the signals from a specific set of neurons in the previous layer, weight each one by some magic factor (2 spoonfuls of this and a pinch of that), shake them together into a single blended number, and then send not this number or a proportional number, but a number that's related by some sort of nonlinear formula to the blended number. One can think of this last step as analogous to "cooking": one combines the ingredients according to the recipe, then (depending on the type of neuron) one bakes, boils, roasts, fries or steams them into something which will in turn become an ingredient for many more recipes. Probably there are some complicated gourmet dishes which involve a similar series of cookings and blendings.

Clearly a key step in all this is those magic weighting factors (e.g. a pinch of salts and 2 pounds of potatoes, rather than the converse). But even more important is the question of how these recipes are written. Who writes the recipes in the brain? God? Darwin? Or the brain itself?

I suspect the last. Indeed, this is the heart of the matter. The recipe that each neuron uses is continuously adjusted to as to improve the taste by the cook - the neuron itself. In my next post I try to explain exactly what goes on in an individual neural connection - a "synapse" - during this recipe-adjustung process. In closing I will just note that the brain is made up of a quadrillion of these synapses - that is
1000,000,000,000,000 of them! The brain is made up of synapses in a way that's similar to a drop of water being made up of H20 molecules. But a synapse is more complicated, and cleverer, than an H20 molecule, and can do many more things.

Saturday, May 10, 2014

Lovers' Beach; the brain continued

In the recent book "The Beach Book: the ultimate guide to all of Eleuthera's 135 beaches" by Sigillo and Ek, to which I've already referred in this blog, Lovers' Beach is rated number one of them all. In our 20 years on Eleuthera Claire and I have never visited this beach, which is rather difficult to access, and much less well known than the other top beaches. But using the book as guide, we were easily able to find it (albeit over a very bad road, for which our Jeep Cherokee is required. The top rating is in some ways justified, even though the beach itself is not as beautiful as quite a few others on the island. This video shows the 360 degree view from the wide grasslands above Lovers' Beach, just north of Gregory Town, and near the hotel "The Cove". There's a dead-end jeep track through the grasslands, which are dotted with Century Plants and Beach Lilies (some in flower). Though only a couple of miles off the main road, the place seems a world apart, with vast horizons and views up and down the coast.  However, the views above Lovers' Beach are amazing, and justify the top rating. This video was taken with a cheap little camera and only has low resolution. I hope to return soon with a better camera.

And now something totally different!


We resume our look at the neocortex, the seat of the mind, in more detail. Here's an image of a slice through part of a monkey brain. The nerve cells (neurons) have been stained in purple, and the neocortex is seen to the right, as a folded sheet of neurons. Since this is a slice the sheet looks more like a folded, concertinering, snake. You can see deep crevasses in the cortical mantle, which are deep infoldings of the sheet. Then underneath this thick purple layer of cells you can see a much paler underlayment - there are no neurons here, but enormous numbers of "wires", or "axons", which are carrying information too and from the overlying sheet of cells. Near the bottom, outlined with a dotted circle, you can see where the cortical sheet fizzles out, forming a curled much thinner but darker sheets called the hippocampus. This is where memories are, at least initially stored - but the memories here are not really complete, more like thumbnails which can trigger a more complete, cortically-based, version.

The sheet of cortical neurons is quite thick (1/3 inch) and is made up of 6 distinct layers. However, the detailed structure of these layers varies quite a bit from one patch of the cortical towel to another. Each patch of cortex seems to process different types of information. For example, the human visual cortex at the back of the head receives (indirectly, via the thalamus, which I will describe shortly) information from the eyes. It then sends this information to other cortical visual area for further processing. These areas are specialized for aspects of visual processing, such as movement or color.

In the center of the image about 1/3 of the way down you can see the visual thalamus, labelled LGd. It has also 6 layers of cells, with alternating layers receiving input from either the left or right eye. Near to the visual thalamus are other thalamic areas, for example labelled VPM,VPJ,LP. These relay other types of information to different patches of the cortex. For example, LP receives partly processed visual infrmation form the primary visual cortex, and sends it back to the cortex (eg to motion or color areas) for further processing.

So, the way the mind digests the world is rather like the way the alimentary canal digests our food: it's done in multiple steps (stomach, duodenum, small and large intestine. Somewhat different types of intellectual "enzymes" are applied at each step, with the net result being not crap but a (sometimes crappy) decision or thought.

What I really want to focus on is the mental digestion process that allows mere "data" (e.g. pixels, supplied by the eye) to lead to ideas. Let's specifically consider object recognition: our ability to glance at an object (e.g. a cup or a hand) and (usually) quickly and almost effortlessly decide what it is.

We are so good at this that it's easy to forget that it's almost a miracle. You can hook a camera up to a supercomputer, and show it a cup or hand, and, however artfully it's programmed, it cannot decide what it is! And it certainly cannot tell you that it's a hand holding a cup! At least now, in 2014. The problem is that while a cup is obvious to us, to a computer it's just a mess of pixels. For images of cups those pixels are different in a specific way from the pixels making up a hand, but this crucial difference ("cupness" versus "handiness") is extremely difficult to define, making it very difficult to program the computer.

Roughly speaking we think that the way the brain (and the cortex in particular) recognises this difference is by large amounts of experience: it has seen many versions of cups and many versions of hands, and it has learned to tell the difference (even without anyone ever saying "these are cups" and "these are hands"). These experiences each generate subtle changes in the connections between the relevant neurons (e.g in the various cortical visual areas mentioned above), such that as information is passed from one set of neurons to another, it's gradually transformed. In the original pixel-based version in the eye, there are no neurons which fire exclusively in response to cups or hands, but somewhere deep in the cortex (I mean, after many stages of cortical digestion) there are neurons that respond only to cups and others that respond only to hands (and others which respond to hands-holding-cups).

This not only works for relatively simple tasks like object reognition, but also, though more painstakingly, for more subtle things like deciding where to dine out tonight, how to purchases that delicious cake, who to marry and figuring out how the brain works.

At this point my reader might start to feel uncomfortable: am I saying that love, and science, and religion, is "nothing other" than the firing of certain neurons? And that furthermore these patterned firings are determined by a purely mechanical, automatic, digestion-like process involving changes in the numbers and strengths of neural connections? The soul boils down to "connectoplasm" (the sneering term used by Steven Pinker in his popular but weighty tome "How the Mind Works"?

In a nutshell I believe this is true, but that the truth is far more amazing than the alternatives, such as those proposed by Pinker or the Pope.....................

Friday, May 9, 2014

Calypso's Internet Cafe; a little good news

Midway between the 3 houses at Calypso lies a grove of trees (palms, tropical almond and gum elemis) and inside this shady grove there's a clearing where we used to have seating for internet users - our wifi internet signal would not reach all the way from our house to the other 2, because of the concrete walls and large distances. I landscaped this area with various plants, such as heliconia, palms and ti plants. The above video shows a brief glimpse of this area.
My spot of good news has nothing to do with the hummingbird sanctuary, or the lawsuit, about which I've heard nothing new. Like everyone I actually have to work - teaching at Stony Brook University in the fall semester, and conducting a program of scientific work. As some of you know my scientific research is about the brain - in a nutshell, how does it work? The good news is that a technical scientific paper that we have been working on for several years was recently accepted for publication by a prestigious journal, "Biological Cybernetics". The work is rather specialized but I thought that I would try to give a layperson description in my next few posts - accompanied of course by tropical videos and hummingbird news.
The brain is rather complicated, and does many different things, and of course can go wrong in many ways. I am particularly interested in a rather ambitious question: how is it possible for humans, and perhaps some other animals, to actually understand things? Of course this is precisely what scientists try to do: understand things. To me it's perhaps the most fascinating aspect of the brain and its accompanying mind: what is "intelligence" and how is it achieved by the 100 billion nerve cells ("neurons") that compose our brain?
To make this more concrete, I focus on a part of the brain that seems to be particularly linked to intelligence, the cerebral cortex (or "neocortex"). This is the part of the brain that's most highly developed in humans, forming the intricately folded "gray matter" that forms the outer, visible (after opening the skull!) rind of our brain (light pink in the image below). It forms a large crumpled sheet, about the area of a tea-towel, and about a third of an inch thick.This sheet contains about 20 billion neurons - actually only a fraction of the total. However, it seems  that all our conscious thoughts and experiences are mediated by this sheet.

The neocortex recieves information from the rest of the brain, which ultimately derives from our sensory organs (eyes, ears, skin etc). It "processes" this information and send instructions to the rest of the brain, and ultimately to our muscles, so we can move and talk. However, even if the brain has no cortex (for example in non-mammalian animals such as birds and fish), it can still receive sensory information about the world, process it and produce appropriate instructions. But the cortex seems to be able to do this more "intelligently", largely because it's able to incorporate past experiences. In a nutshell, the current sensory information gets interpreted in terms of an internal "model" of how the world functions, so that quite complex behavior is triggered by the sensory stimulation. For example, if you see a delicious but expensive cake in a shop window you don't just smash the window and grab the cake. You decide whether you can afford it, and if not you might save up over many weeks until you can.
Patrick J. Lynch, medical illustrator; C. Carl Jaffe, MD, cardiologist. from

Thursday, May 1, 2014

Century Plant in Flower

On the lawn between "SeaStar" and the ocean there's a large agave or "century plant", whose flower stalk has been growing prodigiously over the last few months, and is now starting to bloom. They are reputed to take a 100 years to flower, though I think 30 is more typical. The flower is about 25 feet high and attracts swarms of insects, bats  and birds, including hummingbirds. After blooming the whole plants dies - indeed, it's already dying, as it pours all its stored energy into the immense flower.