Memory and Cognition

There are several theories about how we create memories and how we use those memories to interact with our worlds.  Take a restaurant as an example.  When you think of a restaurant, a fairly specific memory is used to represent restaurants in general.  Now think of a fast food restaurant.  The image changes.  One theory of cognition is that we create lists that represent different interactions.  For example, we have a script for restaurants so we know what to expect when we go to one.  We enter, wait to be seated, order, eat, pay, leave.  The script is modified to account for different types of restaurants.  in the fast food example, waiting to be seated won’t work.  So, we create a new list to account for it.  In that list, we enter, order, pay, eat, leave.  The other theory of cognition is that we store elements of previous encounters and use those to assemble an appropriate mental picture that we can apply to a specific situation.

The way we recall events and integrate them into our minds isn’t as simple as recording them.  The analogues to memory that we have created, hard drives, web sites, etc. record events in a linear way.  Human memory doesn’t record events in the same way.  Instead of remembering an event like a wedding one instant at a time, we record a representation of the event that we can later recall.  This method of remembering can alter the event in our minds in interesting ways.  Each element of an event is stored in different parts of the brain and then reassembled when we recall it.  Each time we remember a wedding, the mind assembles the different parts together to create a new representation of the event.  In essence, we’re recreating the event each time we remember it.

For the wedding example, the ceremony is broken into different elements.  The visuals sounds, smells, and tactile memories are compiled together from different areas of memory to create the memory that we then recall.  The way that the elements are stored allows the mind to free associate those parts with other memories that can then impact the recollection of the whole.  When you recall a wedding, the smell of the flowers can be influenced by other memories that include smells.  A trip to an arboretum can influence the wedding memory in subtle ways.  Discrete elements of the arboretum won’t intrude on the wedding memory, the mind would recognize those parts as being out of place in the wedding memory.  Instead, the sensations and smells of the arboretum can influence the recollection of the wedding.  When the mind assembles the wedding memory, it pulls the smells from the same area that stores the smell memories of the arboretum.  In doing so, the two memory fragments influence each other.  The memory of the arboretum would likewise be influenced by memory fragments from a wedding.

When the mind assembles a memory, it has to free associate within each part of the memory to assemble to whole.  Each sense, smell, touch, sight, sounds, and taste has its own area.  As the mind recalls each sense, other memory fragments can influence how we recall each element of the whole.  This is one of the reasons why eye witness testimony can be problematic.  When the witness tries to assemble the memory of an event, other experiences can influence how that memory is assembled.  Since the mind essentially creates the memory each time it is recalled, that recollection can drift over time.  As other experiences change the memory, a discrete memory can start to change the more we recall it.  That’s why police want to get eye witness testimony when it’s “fresh” and people say that the first impression is usually the right one.  It’s not necessarily true, but it does leave the memory less time to be affected by other experiences and memory fragments.

The list and fragment theories of memory aren’t exclusive to each other.  We could use memory fragments to create the lists dynamically.  The list theory is tempting because that is the way it feels when we go to a place like a restaurant.  We create a script that we expect to follow throughout the whole episode.  How we create the list may be more interesting than the list itself.  In many ways, every memory is the culmination of all our experiences.

Reinstating SSRI use during withdrawal

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You decide that you want to wean off an SSRI. The reason can vary.  Perhaps you want to see what you’re like without the drug.  Perhaps you think you’ve outgrown whatever problem prompted you to take an SSRI in the first place.  Perhaps the drug no longer works like it did before.  At first, your doctor is taken aback and tries to convince you to continue taking the drug.  Eventually, he or she tells you that it’s relatively simple to get off an SSRI.  A doctor’s schedule usually includes skipping days and reducing the dosage by 25% every 10 days until you’re down to 0.  For many people, that schedule will work, but a significant percentage can’t tolerate a fast weaning schedule.  These people quickly start to feel withdrawal symptoms that can vary from mild to severe.  Persisting in a doctor’s weaning schedule can eventually turn mild symptoms into severe symptoms.  The brain reacts to lower dosages of SSRI at its own schedule, not ours.  There is a lag between a lowered dosage and the onset of symptoms that can catch up with you after several drops.  The result is that you feel the effects of several dosage drops all at once.  In worst cases, patients can experience rage, anxiety, fear, even psychotic symptoms.  The best way to wean off an SSRI is to do it very slowly.  Most people who taper off an SSRI do it very quickly at first.  It’s not until symptoms appear that they question the schedule.

Once withdrawal symptoms have appeared, the nature of SSRI use has changed.  There is a point where you put yourself on a track to wean off the drug and can’t really get back to the previous state of SSRI use.  You can take your original dose, but the effect will be different.  Instead of creating the mental environment that you experienced before, it’s now a mix of withdrawal and the SSRI numbness.  Once you’ve experienced a mental state without an SSRI, it’s very hard to go back.  Just as you’re very aware of the effects of withdrawal, restarting an SSRI makes you very aware of the effects of the drug.  Reinstating an SSRI is a mixed bag.  Deciding to start back on an SSRI should be done carefully.  Be prepared to experience some form of withdrawal symptoms as well as the general slowing of mental functions that accompanies SSRI use.  Reinstating should be done to prevent the worst withdrawal symptoms and provide some relief from symptoms that threaten your well being.  It is an opportunity to slowly wean off the drug after weaning too quickly on your first try.

Reinstating an SSRI should not be viewed as a permanent thing.  It’s another step in weaning off of the drug.  It’s very difficult to try taking another drug to treat withdrawal symptoms.  Often, you will get the start up effects of the new drug, as well as the withdrawal symptoms of the last drug.  It’s best to restart the same SSRI you were taking before.  As an example, say you were taking 40mg/day of Paxil for 5 years.  You begin tapering as recommended and reach 0mg/day after 2 months.  At about the 3 or 4 month point, you feel that your well being is in jeopardy.  Normally, the brain would adjust to reductions in Paxil at about 10% each 4-6 weeks.  After 4 months, your brain would be expecting about 20mg/day.  You can reinstate at 20 mg/day, which should mitigate the worst withdrawal symptoms.  After a month, the worst withdrawal symptoms should dissipate and you can continue weaning off the drug at a slower rate.  The next step should be about 18mg/day.  After another month to six weeks, you can move to 16.2mg/day.  Weaning 10% each month or so will eventually bring you down to 0mg/day with fewer withdrawal symptoms.  The slower schedule does not eliminate withdrawal, but it should allow you to live a mostly normal life while doing it.  It’s very difficult to measure pills to that precision, but small changes in dosage can have large effects on withdrawal symptoms.

In order to decide what dosage to reinstate at, take your previous maximum dosage and reduce that number by 10% for each month since you started weaning.  Since your goal is to wean off of an SSRI, you don’t want to start at too high a dose, but at the same time, you don’t want to start at too low a dose.  A low dose reinstatement will take longer to reach stability, which will extend the whole process of tapering.  It’s very tempting to restart at a low dose.  One of the common feelings for people who are weaning off an SSRI is that they just want to be done with it as quickly as possible.  It’s disconcerting to realize that you’ve been “hooked” on this drug for a long time when you thought it was just a therapeutic drug.  SSRI weaning is a long process, often feeling interminable.  It’s important to stick to a slow schedule, though.  Quality of life is more important than the larger goal of being SSRI free, which will happen eventually.

How SSRI work in withdrawal


Neurons in the brain use both electrical and chemical signals to work.  When a neuron is stimulated, it fires electrically.  This stimulates the release of neurotransmitters at the end of the neuron.  These chemicals flow in the gap between neurons until they bind to receptors on another neuron.  Once enough neurotransmitters have attached to the next neuron, it stimulates that neuron to fire electrically, and the process continues.  SSRI affect the chemical part of this process.  Chemically, SSRI mimic the neurotransmitter Serotonin on one side of the molecule, but are different, otherwise.  When it binds to a receptor, instead of activating that receptor, it blocks it.  These receptors absorb excess Serotonin and store it in the neuron.  By blocking the absorption of Serotonin, more of this neurotransmitter stays in the gap between neurons.  The theory is that having more Serotonin available to stimulate new neurons improves mood.

As receptors that are stimulated by Serotonin are blocked, less of the neurotransmitter is absorbed back into neurons.  The brain responds to this lack of stored Serotonin by creating new networks of neurons in an attempt to reestablish the old state of function.  These new receptors are in turn blocked by the SSRI.  As the process continues, the dosage of an SSRI prescription may be increased to counteract the brain’s attempts to restore the old functional state.  Patients refer to this as “poop out”.  It’s similar to the tolerance that other drug users experience.  The difference is that most illegal drugs act on a wide range of neurotransmitters, whereas SSRI target Serotonin specifically.

In withdrawal, the blocking action of the SSRI is removed, and the excess networks of neurons are able to absorb Serotonin again.  Since the brain has been trying to balance against reduced absorption capacity, the result is over absorption.  Serotonin is closely linked to emotions and mood.  The over absorption of Serotonin can lead to extreme fluctuations in mood and even create symptoms in the patient that mimic serious mental illnesses.  Psychosis, anxiety, fear, and even suicidal thoughts are not uncommon.  It takes a long time for the brain to re balance to the new amount of Serotonin.  The brain once again rewires itself and reduces its capacity to absorb Serotonin.  During this rewiring, moods and emotions can fluctuate.  Many patients withdrawaling from an SSRI report that their mood can be different from day to day.  This most likely reflects the fluctuations in available Serotonin.

Serotonin doesn’t just exist in the brain.  There are neuron like cells throughout the body.  Some have described the neurons in the gut as a belly brain.  They’re not as organized as the neurons in the brain and serve different purposes, but the analogy is fairly accurate.  Serotonin is produced in the gut and migrates to the brain where it is used as a neurotransmitter.  The same Serotonin balancing process that occurs in the brain happens in other parts of the body.  SSRI withdrawal can have impacts on many parts of the body.  Along with mood fluctuations, it can cause muscle twitching, stomach aches, gastrointestinal problems.  The effect of blocking Serotonin in the gut may also be linked to weight gain, which is a very common side effect of SSRI use.

SSRI withdrawal can present symptoms that are very close to other diseases.  Doctors who see these symptoms often misdiagnose withdrawal as a new illness or the re emergence of an existing illness.  The diagnostic problem is one of scale.  Anxiety, fear, anger, and even psychosis are present in all human emotions to a small degree.  In withdrawal, these emotions become unnaturally amplified.  An event that would normally produce mild anxiety produces debilitating anxiety in withdrawal.  It’s not until the brain has completed balancing for the new state of Serotonin absorption and release that emotions once again return to the normal baseline.  This problem is further complicated in patients who have pre existing conditions that affect these emotions.  Often, doctors will prescribe new drugs that compound the problems of withdrawal.  Instead of allowing the brain to balance itself, a new chemical is introduced, with new effects and changes to the brain.  Introducing new changes to the brain while it is trying to deal with existing changes can cause a spiral of new symptoms and diagnoses that put the patient on a tract to taking a cocktail of drugs, each meant to treat the effects of the previous drug.

The safest way to stop taking an SSRI is to do so very slowly.  By slowly weaning off an SSRI, the brain has enough time to consolidate the changes in Serotonin absorption and production.  Instead of absorbing the majority of Serotonin in a short time, the brain has the opportunity to deactivate the excess receptors that cause a lack of available Serotonin.  Most doctors and drug manufacturers recommend reducing SSRI dosages by large amounts.  Most tapering schedules only last a month or two.  This time frame is too short for the brain to adjust.  It took a long time for neurons to extend themselves into new areas in the attempt to absorb Serotonin.  Likewise, it takes a long time for the brain to change the structure of neurons so that the old functional state is achieved.  The tapering period doesn’t have to last as long as the original treatment, but it does need to be longer than most recommendations.  10% reductions in dosage each 4-6 weeks is usually sufficient to allow the brain to adjust slowly.  For example, a patient taking 40mg/day would reduce to 36mg/day in the first month, then 32.4mg/day in the second month, continuing to reduce 10% from the last dose.  It’s difficult to measure pills to this granularity, but being as precise as possible is important to reducing withdrawal symptoms.

Hunting a 400 Million Year old Scorpion

A Devonian Trilobite

I’ve loved geology for a long time.  It’s satisfying to know why that hill is there.  I took a field trip in college once.  As we were driving up a hill, my Geology professor stood up in the bus. “Notice how this hill is very steep on the North side, and gently sloping on the south side?  This is a glacial Moraine.  The glacier gathered a pile of rubble from Canada and depositied it here.”  I didn’t stick with geology as a major.  That was the only Geology class I took in school.  I didn’t realize how much of a lasting interest it would become later in my life.  It didn’t help that Geo 101 met at 8AM MWF freshman year.

I think this is a Lichida Trilobite, early Devonian

It took about 10 years for me get interested in Geology and Paleontology.  When I started looking around, I realized that upstate New York is a really interesting place to look for fossils.  The same glaciers that littered next to the mall stripped away a lot of layers.  All the history that sat there for millions of years was scraped away by the glaciers in the last 100,000.  What’s left are some of the first eras of life on this planet.  Upstate New York has two major eras of geology right at the surface.  The Devonian era sits on top of the Silurian.  Upstate New York was under a shallow sea near the Equator during those eras.

 The state fossil of New York is the Euypterid (Yes, there’s a state fossil, your state has one, too).  I’ve been looking for a good example of a Eurypterid for years. I have a couple bits here and there, and another one that’s squashed, but not enough to convince anyone other than my wishful thinking.  It’s not surprising that I haven’t found a good one, yet.  99.9% of the animals that lived on Earth left no remains at all.  In order to form a fossil, the body needs to be covered quickly by a stable matrix (mud, silt, etc.)  Then water needs to leech into the bones or carapace, replacing the organic material with more permanent minerals.  It’s amazing how intricate and detailed a fossil can be considering how they’re created.  Scientists can count the number of fossilized pores on an insect’s leg.


I think this is a Crinoid, Devonian – present

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 My first fossil preparation box

I’ve been a little reluctant to clean up any of the fossils I’ve found.  Even though I bring them home two knapsacks at a time, it doesn’t diminish the feeling that each one is unique.  Each one lived its life, died, then plate tectonics carried it half way around the world to wind up in my display case.  Who am I to come along with a rotary tool or a pick?  I’m getting over it.  The Trilobite at the top of this story is what convinced me.  It’s a solid impression that just needs a little cleaning up to be really special.


The fossil bearing strata in this hill were exposed by a railroad line that has now been abandoned

I have two or three sites that I go to regularly. One is a commercial fossil mine, the others are abandoned railroads or quarries. Any place where man has cut into the ground can be a good fossil site. My favorite is an old railroad that passed right through the middle of a hill near East Bethany, New York. The excavation exposed the hill from the late Devonian all the way back to the Early Silurian. The last time I was there, I was able to find a major extinction event.  I’ll have to go back to find out which specific one it is.  All I know right now, is it happened in the early Devonian.  I feel like I’m inching my way towards understanding this science.

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A lot of people have told me that I’m wasting my time with this hobby.  How can I hope to master something that takes years of study to understand?  I don’t feel like I need to master Paleontology, you’ll notice that I’m still making guesses when I identify what I find.  This is an incredibly complicated subject that uses equipment ranging from backhoes to electron microscopes.  I don’t have either, so I’m not likely to break any new scientific ground.   Like those world travelling Trilobites, it’s the process that’s important.
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Two Brachiopods, I think

Culturally Biased Bottom Up Processing

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Bottom Up Processing describes the process that our brains use to react to sudden stimuli.  When you suddenly hear a doorbell or alarm clock in a commercial and pay attention, that’s bottom up processing.  By using the most widely distributed doorbell tone, the advertising company can almost guarantee that it will affect everyone.  Bottom up processing is a hold over from the time when we had more primitive brains.  When we perceive a threat or a large stimulus input, the primitive part of our brains responds by flooding the brain with neural transmitters and adrenaline.  It’s a very crude way of dealing with threats, and it has some implications for us, now that we have more advanced brains.  An analogy would be opening a newer document with an old word processor.  The information is included, but it comes with a lot of other garbage that has to be sorted through.  The effect of flooding the decision making parts of our brains with adrenaline and transmitting chemicals is to amplify every thought.  Notions that would normally seem ridiculous get the same credence in our minds as our regular, rational, thoughts.

I think that this psychology plays into the phenomenon of Suicide by cop.  The perpetrator is in a temporary, heightened mental state where irrational thoughts of suicide begin to take on the guise of normal, rational thought.  The conscious part of our minds that makes decisions is overwhelmed by the power of these thoughts.  Each thought is powered and amplified to the point where it dominates the conscious mind.  In normal thinking, irrational thoughts sometime float to the surface, but are dismissed or used as starting points to come to a rational decision.  An auto worker who is laid off may ponder a violent hostage situation, but wind up picketing in front of the plant as a rational alternative.  In bottom up processing, the give and take that sorts through irrational thoughts to reach an acceptable conclusion is short circuited, and a normally stable personality may attack police.

Fight or Flight is just the most conspicuous example of bottom up processing.  We experience it in smaller ways every day.  Like the doorbell example, our thoughts, and the weight we give to each one, can be affected by outside stimuli.  After a person is in a heightened sense of awareness, injecting a thought and having it remain important in the mind of the viewer is relatively easy.  The nature of the stimulus determines which set of culture touchstones you’ll be tapping into.  Fed Ex uses bright primary or secondary colors in their logo as the bottom up trigger.  Then they inject the thought of movement by creating an arrow between the E and X.  It’s a mostly harmless use of bottom up processing to promote a brand.  The arrow doesn’t have to be a conscious thing for the viewer, it’s included in the small heightening of senses that the viewer experiences.  By triggering bottom up processing, the viewer interprets the whole sign without relying on their normal check and balance system to evaluate what they see.

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In a high school DWI demonstration, two cars are involved in a mock collision.  Rescue personnel cut the car apart with the jaws of life and remove the driver, who has died in this demonstration.  The mother arrives distraught while the driver is put into a hearse and driven away.  The bottom up trigger is cutting apart the cars.  Using the jaws of life is loud and produces a lot of vibrations that the crowd can see, hear, and feel.  The crowd is now in a heightened state, and open to suggestion.  The commentator, who has been narrating the scene, now uses that to drive home the purpose of the demonstration… drive safe after the prom.  By creating a mental state where the crowd doesn’t discriminate between thoughts and gives each one equal weight, the repeated message from the commentator doesn’t compete as much with other thoughts (I’m a safe driver, that wouldn’t happen to me).  The “it won’t happen to me” thought has already been excluded by the choice of the bottom up trigger.  Telling yourself it won’t happen to you is negated by the chopped up car sitting right in front of you.

New East Bethany Fossils

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I went back to the East Bethany fossil site yesterday.  I came home with about 20 pounds of rough rocks from the early Devonian and late Silurian periods.  The East Bethany site is an abandoned railroad right of way that cut through a hill.  The path goes right through the middle of the hill, so it’s very easy to move between geological periods.  When I work the hill, I start near the top, which is well into the Devonian period.  I cut a step into the hill to stand on, then dig a pit in front of me.  There is about 12 inches of topsoil over the fossil bearing shales.  Once I’ve collected some fossils from the first pit, I slide down the hill a bit, cut a new step, and use my old step as the start for a new pit.  Repeating this all the way down the hill yields regular samples from several time periods.

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Another good idea is to look through the tailings that other fossil hunters leave near their pits.  These rocks might not have the specific fossils the other digger was looking for or they might have been encased in mud and needed some rain to clean them off.  I’ve found a couple good fossils on the surface next to an old pit.

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New York State is doing road work on the section of Route 20 that goes by the East Bethany site. has a couple projects listed for the Bethany/Batavia area.  I had to take a very long detour to get there heading West on Route 20.  I think the project is just getting started because I was able to take Route 20 Eastbound to get back home.  Like everything else in that part of New York State, it’s always about a mile further than you thought it would be.

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There are two hill faces that contain fossils at the site.  The south face (facing North) is much wetter that the North face (facing South)  The shale layers are very soft and fragile here.  It’s easier to dig, but you have to take great care when removing slabs of rock or they will crumble.  They become quite brittle after they dry.  The North face (facing South) has a harder topsoil layer, and the shale layers are generally drier.  It’s easier to pull a large slab out of this hill.  About two thirds of the way up the hill, there is a marked transition and extinction layer.  The deposit changes from a freshwater shale to a harder rock.  Chert, I think.  I think it happened in the Early Devonian period.  I didn’t keep my samples separate enough to create a fine timeline.  I’m going to bring several bags with me and keep each layer separate next time I go.

Saturday with Ted

I’ve been reading about angular momentum and gravity lately.  They seem related to me, like Magnetism and Electricity are related.  Einstein disproved one of Newton’s ideas that the Universe has a stable gravitational foundation.  We seem steady enough here on Earth, but our planet is orbiting our sun, which is orbiting in our galaxy, which is orbiting the local group of galaxies, etc, etc.  No matter how far we look, there doesn’t seem to be a grand tabletop that the Universe is unfolding on.  We all float along in a Bubble we call the Universe, seemingly disconnected from whatever lies beyond.  That poses a problem, though.  Gravity should be much stronger in a universe like that.  Magnetism is a strong force, much stronger than gravity.  After all, a small fridge magnet can withstand the pulling of the entire Earth and not fall off.  Where does all that gravity go?

The theory is that gravity as a force is carried by gravitons, a fundamental particle.  These particles are 2 dimensional, so they can pass from the 4 dimensions we’re used to : Height, width, depth, and time… into some or all of the 7 other dimensions out there.  Since it’s not in our perceivable dimensions anymore, it doesn’t exist for us.  It’s kind of hard to envision it, even the simplified versions these guys talk about.