Showing posts with label memory maintenance. Show all posts
Showing posts with label memory maintenance. Show all posts

Tuesday, July 2, 2024

The Mythology of "Memory Maintenance Molecules"

 In an article at the Nautilus web site, scientist Ken Richardson suggests that his fellow scientists have been guilty of some molecular mythology. He points out that scientists have repeatedly used “action verbs” in describing DNA, telling us that inside DNA are genes that “act,” “behave,” “direct,” “control,” “design,” are “responsible for,” and so forth. But then Richardson tells us “a counter-narrative is building” to correct such erroneous ideas, and then gives us reasons for thinking that genes are merely passive chemical units that do no such things.

Another example of molecule mythology involves a protein called PKMzeta. Some neuroscientists have suggested that PKMzeta has the ability to make memories last for decades in synapses, even though the proteins that make up synapses are very short-lived (having an average lifetime of two weeks or less). Quite a few of the papers or posts spreading this idea were written or co-written by the same person, Todd C. Sacktor. It is never explained clearly by any such theorists how a protein molecule could perform this great feat of magic. For anyone to explain such a thing clearly, he would first need to have a clear theory of how conceptual memories and episodic memories could be stored in synapses. No neuroscientist has ever presented a clear and explicit theory of any such thing. Neuroscientists merely vaguely tell us that somehow memory storage in a brain occurs through “synapse strengthening,” without presenting any clear theory of how that could be memory storage. 

Of course, if you do not have a clear theory of how memories could be stored (for even a few minutes) in synapses, you cannot possibly have a clear theory as to how some protein molecule such as PKMzeta could possibly cause memories stored in synapses to persist for decades, even though the proteins that make up such synapses are very short-lived, lasting an average of less than two weeks. Trying to defend against the charge that synapses are totally unsuitable for storing memories for decades, because of the short lifetimes of the proteins that make up synapses, a scientific paper states, “As long as PKMZ [PKMzeta] remains active and there is an absence of forces which terminate its activity (such as LTD), it will continue to sustain the biochemical changes at the synapse which serve as the neurobiological basis of memory, allowing the memory to persist for durations far exceeding the turnover of its component molecules.” But how could such a miracle of persistence occur, which would be like a message written in wet sand at the seashore persisting for decades, even though the wet sand was being replaced and written over whenever the tide came in? The science paper does not tell us.

Again, we have the case of an “action verb” inappropriately used to describe a molecule. We are told that PKMzeta has a “sustain” super-power allowing it to preserve fantastically complicated information supposedly stored externally in synapses made up of short-lived molecules that are constantly being replaced. There is nothing in the structure of PKMzeta that should cause us to believe it can do any such thing. No theorist has presented an explicit theory as to how anything like PKMzeta could preserve a memory. Such theorists may sometimes present chemical details to impress us, but such details do not constitute a theory unless a theorist gives explicit examples of precisely how specific memories (such as someone's memory of seeing Paris or someone's memory of details learned about World War I) could be permanently stored with the aid of PKMzeta.  No theorist has done any such thing. 

I suppose that if a PKMzeta molecule were able to cause memories to persist despite rapid protein turnover,  we might imagine it as some kind of "genius" molecule that has thoughts like this:

Oh, my goodness, I see that a memory is starting to degrade because of protein turnover! The memory now states, "Ottawa is the capitol of," which isn't even a full English sentence. Why, I'd better synthesize some new proteins to fill in for those proteins that died,  so there can be a nice complete English sentence. Now, what was that country that Ottawa is the capital of?  

Of course, anything the slightest bit like this is very hard to believe in. It would seem that the most minimal requirements that a molecule would have to fulfill in order to be a "memory maintenance molecule" would be the following:

(1) The molecule would have to somehow know whenever a particular protein molecule (that was part of a memory stored in a synapse) had died or disappeared because of the short lifespans of protein molecules.
(2) The molecule would have to somehow cause a replacement protein of the same type to appear in the same place as the vanished molecule, so that the memory did not degrade. 

The problem is that no one can envision a credible scenario under which a molecule could have either of these powers. To imagine how much of a miracle it would be for memories to persist despite constant protein turnover,  you can imagine a homeowner with ten picnic tables in his backyard, each of which is filled with leaves on which a word or two is written. Imagine these leaves spell out narratives, factual information, and ideas. But the problem is that about one day in three there are winds blowing the leaves off of the tables, and scattering them far away. Also, the leaves don't last longer than a year, because they tend to crumble. Now imagine the homeowner has to keep all this information preserved in the leaves, not just for a few nights but for 50 years. That would be a mountainous job.  An equally mountainous job would have to be done if memories were to be preserved in brains despite constant protein turnover causing proteins to persist an average of less than two weeks, and no one has explained how a molecule could possibly do such a feat.  Since synapses face not only rapid protein turnover inside them but also the problem that synapses don't last for longer than a year or two,  they have the same "double degradation" problem that such a homeowner would have with his information written on leaves. 




In the article here, a PKMzeta enthusiast is asked to explain how PKMzeta could cause memories to persist. The scientist gives a lengthy answer which fails to explain how PKMzeta could do such a thing. He merely says "a cluster of PKMzeta molecules can keep themselves turned on perpetually," and then claims that this supposed ability "is a plausible mechanism for memory persistence," without justifying that claim. This fragmentary theorizing is just hand waving. It has never been demonstrated that any cluster of PKMzeta molecules is capable of storing any information (such as a list of words) for a period as long as a month.  We can imagine hypothetical lab experiments that might try to show such a thing, but they have never been done. The paper here refers to "900 synaptic proteins." PKMzeta is only one of those 900 proteins in synapses, being no more common in synapses than an average synapse protein. You don't solve the "short lifetime of proteins" problem by trying to argue that one in 900 of those proteins might somehow have some stability.  As for the scientist's use of the word "plausible," it has been noted by others that "plausible" is the most abused word in theoretical science discourse, and that scientists often carelessly use the word "plausible" without ever doing anything at all to show a likelihood. 

But the PKMzeta enthusiasts have done a few studies which they claim lends credibility to their claims. I will describe a typical such study. A small number of mice are injected with something that suppresses the PKMzeta molecules in their body (or perhaps they are genetically engineered so that they don't have any PKMzeta). Memory experiments are then done. It is sometimes claimed that such mice perform not as well as normal mice. Such experiments have been hailed as support for the “memory maintenance” claims about PKMzeta.

There are several reasons why such studies do not at all show the claims about PKMzeta are correct. The first is that a result such as I described could never show that PKMzeta can save memories from destruction for years. Whenever memory is tested, it's hard to figure out what the cause is for a discrepancy between two test groups. A difference in a test result might be because (1) PKMzeta is involved in perceiving whatever observation is being tested; (2) or that PKMzeta is involved in memory storage; (3) or that PKMzeta is involved in memory retrieval; (4) or that PKMzeta has something to do with attention or focus or visual perception used in a memory test. A test discrepancy could never tell us which of these things was involved. And if some mice did worse in remembering things without PKMzeta, that might justify the small claim that PKMzeta has something to do with memory, but could never justify the vastly more extravagant claim that PKMzeta is capable of preserving memories for decades.

Another reason why such studies do not at all show the claims about PKMzeta are correct has to do with a general malaise in neuroscience. A general problem in modern neuroscience is the production of papers with marginal results that we cannot trust because of things such as too-small sample sizes and publication bias. Let us imagine that neuroscientists want to prove some idea that fits in with their ideological expectations. A great number of experiments might be done, almost all producing no support for the idea. But perhaps 1 in 20 might produce results marginally supporting the idea, probably because of chance variations in data. Now, today negative results are vastly less likely to get published than positive results. So if 19 researchers get a negative result, conflicting with what neuroscientists hope to get, it could be that 10 of them don't even bother to write up their results as a scientific paper, and that the other 9 do write up a paper but don't get it published (because of the journal bias against negative results). However the one researcher who (by chance) got a positive result will write up his result as a scientific paper. Since it will be a result neuroscientists were hoping to get, he will almost certainly get the result published.

This publication bias is a great problem affecting the reliability of scientific research. Because of it we should follow a precautionary neuroscience rule like this: don't believe something has been established unless the result turns up fairly consistently at a high level of significance, in studies with large sample sizes.

Has this happened in regard to memory experiments involving PKMzeta? Not at all. In 2011 a scientist reported three separate studies showing that inhibiting PKMzeta has no effect on memory if tested between 10 and 15 day after the memory forms.  In 2013 two groups of scientists published results conflicting with claims that PKMzeta might allow memories to persist a long time. One study by a team of scientists used genetically engineered mice that had no PKMzeta. It found that such mice “have no deficits in several hippocampal-dependent learning and memory tasks,” and concluded that PKMzeta is not required for memory or learning. Another study by a different team of scientists found that absence of PKMzeta “does not impair learning and memory in mice.” A 2015 study found that inhibiting PKMzeta has no effect on memory in tests performed 30 days after the memory forms. A 2016 paper also found that that inhibiting PKMzeta has no effect on memory in tests performed 30 days after the memory forms.

Such studies would seem to completely debunk claims that PKMzeta enables memories to persist for decades in synapses despite the short lifetimes in the proteins.

The scientists such as Sacktor who helped to spread the PKMzeta myth have tried to fight back with papers such as this 2016 paper. But in that very paper we see evidence that second-rate science is being used to try to prop up claims about PKMzeta. In Figure 7 the scientists tell us how many mice were used for their experiment involving the memory effects of PKMzeta deprivation. They used only 8 mice per study group. That's way too small a sample size to get a moderately convincing result. It is well known that at least 15 animals per study group should be used to get a moderately convincing result. If you use only 8 animals per study group, there's a very high chance you'll get a false alarm, in which the result is due merely to chance variations rather than a real effect in nature.  In fact, in her post "Why Most Published Neuroscience Studies Are False," neuroscientist Kelly Zalocusky suggests that neuroscientists really should be using 31 animals per study group to get a not-very-strong statistical power of .5, and 60 animals per study group to get a fairly strong statistical power of .8.  Compare these numbers to the 8 animals per study group mentioned in Figure 7 of the Sacktor paper. 

This is the same “too small sample size” problem (discussed here) that plagues very many or most neuroscience experiments involving animals. Neuroscientists have known about this problem for many years, but year after year they continue in their errant ways, foisting upon the public too-small-sample-size studies with low statistical power that don't prove anything because of a high chance of false alarms.

If you look up the PRKCZ gene behind the PKMZeta protein molecule, using this page and this page of the Human Protein Database, you will find no characteristics that seem unusual, and nothing suggesting any superstar status. The pages make no mention of the gene even being used in synapses, telling us that the gene is "mainly localized to the cytosol" and "in addition localized to the plasma membrane."   The very idea of some kind of "superstar protein" or "superstar gene" is contrary to the experience in recent decades of scientists, who have found in general that bodily functions almost always involve the coordinated ballet of very many different genes (typically hundreds of them to accomplish a particular task). 

The 2015 scientific paper here shows that PKMzeta rapidly degrades in synapses. The authors say that therefore a stable amount of PKMzeta "would be difficult to maintain at synapses and store memories over long time scales." The paper tells us “There is growing evidence against a role for PKMzeta in memory.” Figure 9 of the paper also shows that a kind of cousin molecule or "isoform" of PKMzeta (PKC lambda) also quickly degrades, experiencing a 50% loss or degradation every 10 hours. So it seems that there is no truth to the idea of PKMzeta (or PKC lambda) as some magic bullet that allows memories to persist for decades in synapses that are constantly having their proteins replaced.

Where does that leave neuroscientists? It leaves them without a leg to stand on in their claims that memories are stored in brains. Based on everything we know about synapses, there is no reason to believe that synapses are capable of storing a memory for even a month, let alone the 50 years that is how long older humans can remember things. As discussed here and here, equally grave problems prevent scientists from creating any credible account of how memories could be encoded into neural states or how seldom-retrieved facts learned many years ago could be instantaneously recalled from a brain that seems to lack any capability for fast look-ups from exact neural positions. We also know (as discussed here and here) that massive damage can occur to brains (such as surgical removal of half of a brain) while producing little effect on memory, which would seem to be impossible if memories are stored in brains. How long before we realize that human memory cannot be a neural thing, but must be a psychic or spiritual phenomenon?

Some people tell tall tales about the protein CAMKII similar to the tall tales told about PKMZeta. We are sometimes told that some alleged autophosphorlyation of CAMKII can help explain stable memories. Most of the reasons I have cited against PKMZeta also apply with equal strength to CAMKII. At this link we are told an experiment debunked the idea that  autophosphorlyation of CAMKII has a role in memory storage.  The lifetime of a CAMKII molecule is only 30 hours, according to this source. The book here makes this statement:

"In the mid-1980's there was much excitement about the idea that autophosphorlyated CaMKII might serve as a self-perpetuating signal that could subserve permanent memory storage. However, a variety of experimental results generated since then suggests that perpetual activation of CaMKII does not occur with LTP-inducing stimulation or memory storage."

This scientific paper says the following:

"Previous models have suggested that CaMKII functions as a bistable switch that could be the molecular correlate of long-term memory, but experiments have failed to validate these predictions....The CaMKII model system is never bistable at resting calcium concentrations, which suggests that CaMKII activity does not function as the biochemical switch underlying long-term memory."

This recent scientific paper says on page 9, "Overall, the studies reviewed here argue against, but do not completely rule out, a role for persistently self-sustaining CaMKII activity in maintaining" long term memory. Another paper says, "The autophosphorylation of CaMKII, once thought to help maintain long-term changes in synaptic strength, has since been revealed to be rather transient." 

Those who have studied the history of science are familiar with epicycles, a complicated speculation that was introduced into Ptolemy's theory of astronomy, to try to fix cases in which the theory did not match observations. We may say these CaMKII speculations and PKMZeta speculations are epicycles intended to fix the failing synaptic theory of memory storage.  But while the Ptolemaic epicycles were exact speculations, the CaMKII speculations and PKMZeta speculations are very vague, failing to specify any exact theory of memory storage. 

Last week a press release from New York University tried to breath life into the dead horse of the mythology of "memory maintenance molecules." The press release was a glaring example of what constantly occurs these days in university press releases: university PR offices boasting about grand accomplishments that were not actually accomplished. We have the untrue claim that a "new study in the journal Science Advances, conducted by a team of international researchers, has uncovered a biological explanation for long-term memories."  No, the study was just more Questionable Research Practices junk science, a study so poorly designed it is a wonder it got published.  We read this:

"It’s been long-established that neurons store information in memory as the pattern of strong synapses and weak synapses, which determines the connectivity and function of neural networks. However, the molecules in synapses are unstable, continually moving around in the neurons, and wearing out and being replaced in hours to days, thereby raising the question: How, then, can memories be stable for years to decades?"

No, it has not ever been established that " neurons store information in memory as the pattern of strong synapses and weak synapses" : no credible theory of how such a thing could work has ever been advanced, no memory information stored in neurons or synapses has ever been found through microscopic examination, and the instability of synapses (including the short lifetimes of their proteins) is the strongest reason for thinking that it cannot possibly be true that "neurons store information in memory as the pattern of strong synapses and weak synapses." 

The press release makes the groundless claim that the junk science paper it is publicizing shows "that KIBRA is the 'missing link' in long-term memories," referring to a molecule called KIBRA.  The press release makes the groundless claim that "their experiments in the Science Advances paper show that breaking the KIBRA-PKMzeta bond erases old memory."

The study is the study "KIBRA anchoring the action of PKMζ maintains the persistence of memory" which you can read here. We have a very bad example of Questionable Research Practices junk science. The study group sizes used are ridiculously small, with study groups as small as only 4 mice and 6 mice, and the average study group size being only about 7 mice. It is frequently pointed out to neuroscientists that experimental studies involving mice are generally worthless unless they use at least 15 subjects per study group; but neuroscientists keep senselessly continuing to use ridiculously low study group sizes.  Why do they do that? Because it allows them to "mine noise," and report false alarms that would vanish if a decent study group size was used. It's rather like someone trying to prove his prophetic powers by publishing a test in which he correctly predicted whether merely four consecutive coin flips were "heads" or "tails," conveniently failing to publish a larger test of his powers involving how well he predicted 15 consecutive coin flips.  You can get all kinds of false alarms when you use tiny sample sizes. 

low statistical power in neuroscience

The junk science paper above relies crucially on an attempt to measure fear, and the attempt to measure fear was the stupid, unreliable technique of attempting to judge "freezing behavior" in mice. All experimental studies relying on estimations of "freezing behavior" are junk science studies, for the reasons I explain in my post here.  There are good reliable ways of measuring fear in rodents, and whether a mouse still has a memory of something the mouse was trained to fear. One good method is to measure heart rate, which dramatically spikes when a rodent is afraid. Another good method is to detect movements in which a mouse avoids a stimulus an animal was trained to fear. The technique is shown in the diagram below:

good way to measure fear in mice

Attempting to measure whether a rodent remembered something fearful by doing estimates of "freezing behavior" is not a reliable way of measuring fear or memory, but instead an unreliable "see whatever you want to see" affair. All studies hinging on so unreliable a method are junk science studies, including the new study by Sacktor mentioned in the New York University press release. Contrary to the claims by Sacktor in his later paper and the claims in the New York University press release, no robust evidence has been produced to show that inhibiting either the KIPRA molecule or the  PKMζ molecule (PKMzeta) does anything to harm the memory of mice. In the paper and the press release Todd Sacktor tells the tall tales of memory maintenance mythology that he likes to tell, unbelievable tales that are not backed up by any robust experiments. 

Genuine "freezing behavior" in an animal would typically only be an instantaneous thing, lasting only a few seconds. The longer the length of time over which "freezing behavior" is judged, the more unreliable such a judgment is as a basis for judging whether the animal recalled a fearful stimulus. In Sacktor's latest paper discussed above, which you can read here,  fear recall is being judged by someone estimating how much an animal was non-moving over a length of four minutes.  That's a particularly unreliable use of the utterly unreliable technique of judging "freezing behavior" as a method of trying to determine whether recall occurred.  

A 2024 scientific paper makes this candid confession, using the phrase "still not completely understood" when it should be saying "are not at all understood":

"Despite over a hundred years of research, the cellular/molecular mechanisms underlying learning and memory are still not completely understood. Many hypotheses have been proposed, but there is no consensus for any of these."

The paper calls Sacktor's speculations about the  PKMζ molecule (PKMzeta) "very controversial." 

I can give you an example that helps show the difficulty of maintaining stable information from unstable components. Let's suppose a shaving creme company wants to publicize its product. It arranges for a line of people to appear outside of the main branch of the New York Public Library, a line in which each person will be displaying a letter made out of shaving creme. The total line of people will spell out the message: "Sale! 10% off on purchases of Barbisol shaving creme, the world's most comfortable shaving creme."  The letters will look like this, but each letter will rest on the outstretched palms of one person.


The problem is that the shaving creme letters will soon decay. How to keep the advertising message running all day?  There could be a system in which each person stands on a numerical position with a number between 1 and 97. If a person sees his shaving creme letter is disintegrating, he then sends a text message to some phone number, saying something like, "I'm leaving -- I'm at position number 12, and my letter is F."  Then some person getting all these text messages can keep sending one of his helpers to each position mentioned in a message, filling in the letter mentioned in the text message.  Through such a system the message might last all day, even though each letter only lasts for less than an hour. Note well some of the requirements here, which include:

(1) A system for representing words by use of symbolic tokens (the English alphabet). 
(2) Some skill for creating these tokens in shaving creme letters (maybe someone who has practiced this skill). 
(3) An addressing system by which each person in the line knows his ordinal position in the line.
(4) A  message system by which components that are about to fail send out a message to some receiving system notifying it to replace their failing token, telling that receiving system of which token to replace, and what the address was of the token to replace. 

No similar system could ever be possible in the human brain. The human brain has no addresses or position numbers or position notation system or coordinate system. Neurons and synapses have no knowledge of the English alphabet, and no capability of writing synapse states or neuron states corresponding to letters of the English alphabet. A protein about to decay in a synapse would never know it was about to decay, and would never be capable of sending some external receiver a "replace me" message. And such a message could never have the address or position coordinates of a synapse protein to be replaced, because tiny components in the brain have neither  addresses nor position coordinates. When you also  consider that synapses are all entangled in 3D space, making them geometrically more difficult to work with than a simple one-dimensional line, you may start to realize how mythical is the notion that stable memories lasting decades could be made from constantly-replaced components with lifetimes of only a few weeks. 

Postscript: A 2018 paper tells us a little about the appalling state of research practices in research involving rodents:

"There is a crisis in pre-clinical biomedical research
involving laboratory animals. Too many papers publish
results which turn out to be irreproducible. One estimate puts the cost at $28 billion being wasted per annum in the United States alone. The causes of this irreproducibility crisis have not
been fully identified. But it has been known for many
years that experiments are often poorly designed, inadequately analysed, and misreported. A survey of
271 papers chosen at random involving rats, mice
and non-human primates showed that 87% did not
report random allocation of experimental subjects to
the treatments and 86% did not report 'blinding' 
when measuring the results. None of the papers gave
any justification for their choice of sample size, and a
substantial number of papers failed even to state the
sex, age or weight of the animal."

A 2021 paper ("Increasing the statistical power of animal experiments with historical control data" by V. Bonapersona et. al. ) gives us the damning graph below:

poor practices in neuroscience

The graph shows an analysis of 1900+ neuroscience papers. A statistical power of 80% is considered a good goal to reach (when such power is reached there will be about an 80% chance that a reported effect is real). The first graph shows that the average neuroscience paper has a miserably weak statistical power of only about 15%.  The graph on the right shows the number of animals used in these papers, with a median of only about 10 per study group. It is largely because of such low study group sizes that the papers are getting such poor statistical power.  The study group sizes in the Sacktor paper discussed above are sub-standard, even within the dismally poor practices being followed by today's neuroscientists, where the median is a way-too-low number of about 10 animals per study group.  We read this:

"For a common effect size of Hedge’s g= 0.5 (Welch’s independent samples t-test, α=0.05), ten animals per group would correspond to a statistical power of 18%, 30 animals per group to 48% power and 65 animals per group to 81% power...Through a systematic search (Supplementary Notes 1 and 2), we identified a large sample of animal studies in the areas of ‘neuroscience’ and ‘metabolism’ (n...=1,935) that were previously included in meta-analyses (n...=69). These animal studies had an overall median statistical power of 18% (Fig. 1a), which was roughly equal in the two fields (neuroscience, 15%; metabolism, 22%)....We estimated that, at best, 12.5% of a large sample of rodent studies were sufficiently powered (that is, prospective power was larger than 80%). This estimate is a best-case scenario, as it is not yet adjusted for any subsequent multiple testing, experimental bias, P hacking and/or fishing, selective reporting, etc.." 

Postscript: Scientific American has an article covering Sacktor's latest paper, giving us yet another example of its very poor journalism regarding neuroscience research. We have an appalling failure to inform the reader of the most basic facts about Sacktor's latest study. At no point is the reader told that the research merely involved rodents. At no point are we told about the appallingly small study group sizes used, such as only 7 rodents.  Sacktor is allowed to get away with a groundless boast that he "nailed it," and no mention is made of how the study hinged upon an unreliable technique for measuring memory (the faulty judgement of "freezing behavior" discussed above).  The author falls for Sacktor's boasts "hook, line and sinker." 

I may also mention that the study fails to discuss how an effective blinding protocol was followed.  We get a mere sketchy vague  statement that an experimenter judging how much "freezing behavior" occurred was "blind to the conditions," but that does not constitute a description of an effective blinding protocol. When very small study group sizes (such as only seven mice) are used it is easy for a supposedly blind judge to know (by visual recognition) whether or not some animals being analyzed were part of some group that had been chemically treated, and which were desired to be described as acting in a particular way, such as "freezing" more. Effective blinding in an experiment (necessary whenever subjective judgments are made) can only be achieved by following a careful, detailed blinding protocol taking at least a long paragraph to describe; and that apparently did not occur in this study. No reliable measurement or reliable analysis of memory performance has occurred. 

Post-postscript: A perennial promoter of junk neuroscience research, Quanta Magazine had a 2025 article promoting Sacktor's groundless boasts, one with the bogus title "The Molecular Bond That Helps Secure Your Memories." Sacktor's paper with the ridiculously low sample sizes such as only four mice or six mice is passed off as a discovery, with no mention at all of the absurdly low study group sizes used. Another neuroscientist guilty of the same type of very poor research practices (such as the use of way-too-small study group sizes and utterly unreliable "freezing behavior" judgments to try to measure animal recall) is quoted as praising Sacktor's research. Again and again the article uses the word "discovery" or "discovered" for something that was not actually discovered, and again and again the article uses the word "showed" for something that was not actually showed. 

Post-post-postscript: The 2025 paper here states that  "the synaptic turnover rate is as high as 1% per day in the visual cortex." That is a rate of about 100% replacement every four months. If that is the typical rate at which synapses are replaced, synapses cannot be the storage place of memories lasting decades. Quoting an even higher rate of synaptic turnover, the paper here states, "A recent imaging study revealed that the synaptic turnover rate in hippocampal CA1 cells is very high, with an estimated lifetime of 1–2 weeks (Attardo et al., 2015)." 

Sunday, March 19, 2023

Wobbly Hand-Waving Guesswork of the Synapse Memory Theorists

Let us look at a science paper attempting to convince us that memories are stored in synapses. The 2018 paper by Wayne S. Sossin is entitled "Memory Synapses Are Defined by Distinct Molecular Complexes: A Proposal." You should take careful note of the phrase "a proposal" at the end. It indicates the speculative nature of what Sossin writes about. To make a proposal about some possibility typically does not have a hundredth of the worth of making an observation showing the likelihood of such a possibility. 

The abstract of the paper incorrectly states "there are strong evidential and theoretical reasons for believing that memories are stored at synapses." No such reasons exist, but there are very strong reasons for rejecting such a claim, such as the very short lifetimes of the proteins that make up synapses (less than two weeks), and the instability of the dendritic spines such synapses are attached to.  The body of the paper begins by stating, "Most neuroscientists believe that memories are encoded by changing the strength of synaptic connections between neurons (Mayford et al., 2012; Poo et al., 2016)." The two references do not take us to any papers showing that most neuroscientists believe such claims about synapses. It merely takes us to two papers in which a few neuroscientists seem to speak as if they support such claims. 

The claim that most neuroscientists believe such a thing about synapses is a common claim, but it is never well-supported. How could you substantiate such a claim, which is not a claim about synapses themselves, but instead a claim that most neuroscientists believe some particular thing about synapses?  The only way you could do that is by referring to an opinion poll taken of neuroscientists, one that showed that a majority of them believed that memories are stored in synapses. For the opinion poll to be persuasive, it would have to be a secret ballot poll. Any kind of "show of hands" claim would not be persuasive, because there are sociological reasons and psychological reasons why scientists might prefer to publicly act like they are going along with some majority, rather than publicly defying such a majority.  But secret ballot polls of neuroscientists virtually never are done.  We have no actual evidence that a majority of neuroscientists believe that memories are stored in synapses. We merely have quite a few neuroscience papers in which authors claim that most neuroscientists believe such a thing. Even if it were true that most neuroscientists believe that memories are stored in synapses, that would not show the likelihood of such a thing. There are all kinds of sociological and groupthink and "follow the herd" reasons why an erring belief tradition about synapses might arise in the neuroscientist community.

The second sentence of the body of the paper makes a misleading  claim: "The great success of deep learning systems based on units connected by modifiable synaptic weights has greatly increased the confidence that this type of computational structure is a powerful paradigm for learning."  So-called "neural nets" do not use any arrangement matching an arrangement of matter in the brain, and never should have been called "neural nets."  The parts of a neural net that are sometimes called "synaptic weights" but mainly just called "nodes" or "weights" are stable electronic units or software variables that bear no resemblance to unstable non-electronic synapses in the brain. Computerized "deep learning" systems do nothing to substantiate the idea that synapses store memories. 

Without trying to summarize the reasoning of the paper, I can give you a taste of how speculative it is by simply quoting statements in it that use the words "may," "could" or "might":

"The selection of a neuron to participate in a memory may also leave long-lasting transcriptional marks such as changes in histone and DNA methylation, and long-term changes in the organization of the nucleus....If transcription were also required for the maintenance of memory, it would suggest that a form of synaptic tagging may also be important for the maintenance of memory. However, in synaptic tagging the half-life of the tag has been measured to be at most a few hours (Martin et al., 1997; Frey and Morris, 1998b), whereas the half-life of the tag would need to be much longer for it to play a role in the maintenance of memory....Conformational changes induced by the priming phosphorylations may also be important in maintaining binding interactions important for localization of the PKMs and may be important for the ability of these reagents to work as isoform-specific dominant negatives....A model for a positive feedback loop of phosphorylation has been proposed...Compensation for the loss of PKMζ may be due to cleavage of PKCι to PKMι by calpains, although this is purely speculative at present.... Increasing AMPA receptor endocytosis may play a role in active forgetting.... Inhibition of BRAG2 may be a target of persistent kinase phosphorylation (Sacktor, 2011). However, since many forms of LTD require BRAG2 (Scholz et al., 2010), the specific removal of AMPA receptor complexes at memory synapses may also require distinct motifs or adaptors that are regulated by persistent kinase activity in addition to BRAG2....Connection between two neurons may consist of a stable component and a memory component. Removal of either component may be sufficient to reduce synaptic strength and thus compromise memories that depend on this increase in synaptic strength....Memory synapses or memory modules at synapses may be defined through specific trans-synaptic adhesive interactions that align the AMPA receptor complexes specific for memory with specific presynaptic molecular complexes. These presynaptic molecular complexes may also have specializations important for memory...There may be multiple adhesion pairs that define distinct types of memory synapses or memory modules at synapses. One can envision trans-synaptic adhesion as defining what is often referred to in the plasticity literature as a “slot.”...An appealing model would be that as well as causing endocytosis of the AMPA receptors, the 'slot' proteins would also be a target of endocytosis after inhibition of the persistent protein kinase....The concept of a memory synapse remains an unproven hypothesis.  Generating a memory synapse may require multiple rounds of modifications...Both pre-and postsynaptic gene expression may be required to generate specific adhesion proteins that attract specific AMPA receptor complexes and presynaptic specializations,

We also have these statements:

"The dominant negative PKMs could distinguish molecular complexes involved in associative and non-associative LTF, interfering specifically at synapses with one type of complex but not the other,.. Inhibition of persistent kinases in the presynaptic cell could also lead to endocytosis of the presynaptic partner of the adhesion complex."

This speculative gobbledygook does not at all add up to a real theory of how synapses could store memories. All that we have here is some jargon making noises that may sound like an explanation to some people. A real theory of synaptic memory storage would give us specific hypothetical examples describing precisely how some specific learned information (such as the statement "my dog has fleas") could be stored in synapses. We never get such specifics from synaptic memory theorists. We basically get just jargon-laden hand waving, often decorated with poorly documented equations designed to impress us. 

A 2019 paper gives us another example of wobbly hand-waving guesswork. We read this:

"A signal complex like CaMKII/Tiam1 is proposed as a molecular memory... CaMKII may also act as an activity-dependent scaffold to assemble proteins at the synapse in addition to F-actin binding through CaMKIIβ....CaMKIIβ may play a structural role in targeting the RAKECs of CaMKII in the synapses via actin...These knock-in CaMKIIα molecules may have a dominant negative effect to form RAKECs in the synapses...These kinases may form a RAKEC with their specific substrates or upstream kinases....The RAKEC may be a general mechanism for the maintenance of the biochemical activity of kinase and its substrate...Synaptic localization of βPIX may also be regulated by LLPS."

Then we have in the same paper these uses of the word "could"

"Actived [sic] CaMKII could be diluted by inactive CaMKII from the cytosol....Upregulation of the CaMKIIα protein after LTP could further dilute activated CaMKIIα...The regulation of F-actin could be a candidate for LTP maintenance....CaMKII could act as an activity-dependent scaffold for assembling signaling proteins in the synapse...The interaction of CaMKII with synaptic proteins, including NMDAR, could be phase-separated from other synaptic proteins...The RAKEC between Tiam1 and CaMKII may serve not only as signal machinery to maintain Rac1 activity but could also form the LLPS, in which many synaptic signaling proteins are assembled together or are put on standby to act efficiently and effectively to maintain LTP for longer periods."

A diagram in the paper has a circle with "CAMKII" inside it, surrounded by eight text boxes, five of which have a question mark at the end. I cannot recall ever seeing so many question marks in a scientific diagram.  At the bottom of the diagram we see an arrow pointing to the words "memory maintenance," which hardly makes sense given that the average lifetime of a  CAMKII protein molecule is a mere 30 hours (according to the paper here). 

There is a reason why both papers quoted above are unsubstantial. You cannot have a substantial theory of the long-term preservation of memories in the human brain (with memories being preserved for decades) unless you first have a detailed theory of how human learned knowledge could be represented in a brain. Neither of these papers advance any such theory or endorse any such theory.  There simply does not exist a detailed theory of how the many diverse forms of human learned knowledge and human experience could be represented in a brain. If you don't have such a theory, any set of speculations about "memory maintenance" or the lifelong preservation of memories in a brain is a "castle on a cloud" affair rather like a penthouse apartment without any apartment building underneath it. 

One of the papers above makes a speculative appeal to a "feedback loop." Appeals to the possibility of such "feedback loops" appear often in the speculative papers of brain memory theorists. Such appeals are sterile and futile, being based on the erroneous simplistic nonsense that "synapse strengthening" can explain memory. To explain a physical storage of human experiences and learned information, you would need some incredibly complicated and multifaceted system (unlike any yet discovered in the brain) that would need to be a billion times too complex to be centered around mere strengthening.  Having foolishly got in bed with the vacuous notion that memories can be explained by some mere strengthening, our synapse theorists then think that they can account for the gigantic discrepancy between the short lifetimes of synapses and their dendritic spines and the short lifetimes of synapse proteins, by speculating about "feedback loops" that might preserve the strength of some synapse. But since the whole original idea that a mere strength level could store a memory was very foolish, this appeal to never-discovered "feedback loops" preserving synapse strength is equally foolish. Similarly, thinking that information can be stored in clouds is foolish, so thinking that information could be preserved in clouds long-term through "cloud-to-cloud information transfer" is an idea that is futile and sterile.  

In the papers presenting such speculations, we typically see a simple-looking diagram mentioning a feedback loop. The diagram below gives you a better idea of the kind of thing that would have to be going on for "feedback loops" to be preserving information in unstable synapses. Every little token of information would need to have its own special "feedback loop" to preserve that particular type of information. So the stable storage of as simple a piece of information as "my dog has fleas" in unstable synapses would require many types of feedback loops, as shown in the diagram below:

memory maintenance feedback loop

You may realize how utterly nonsensical it is to imagine such a thing when you realize that the chemical units imagined to implement these feedback loops would be short-lived chemicals, and that synapses are attached to dendritic spines that do not last for years, and often don't even last for six months.  So such "feedback loops" would themselves be very unstable, and could never account for stable memories that last for decades. 

One of the papers quoted above speculates that CAMKII might be the key to some miracle of "memory maintenance" by which memories last for decades while stored in synapses that don't last for years, built of proteins that last for less than two weeks. Contrary to such speculations, a 2019 paper states, "Overall, the studies reviewed here argue against, but do not completely rule out, a role for persistently self-sustaining CaMKII activity in maintaining LTP and LTM [long-term memory]." A speculative appeal has also been made to the idea that a protein  PKCζ might help cause such a miracle of memory maintenance, but a paper says that "LTP and memory are retained in PKCζ knockout mice," referring to mice genetically modified to have no such  PKCζ.  The paper tells us, " In the strongest sense of ‘necessity’ for LTP/memory maintenance, therefore, neither CaMKII nor PKMζ meets the criterion."

The papers quoted above were from a 2018 paper and 2019 paper, and in 2023 we still have nothing more weighty to substantiate claims that memories are stored in synapses. A 2022 paper makes this confession:

"We are still far from identifying the 'double helix' of memory—if one even exists. We do not have a clear idea of how long-term, specific information may be stored in the brain, into separate engrams that can be reactivated when relevant."

Another 2022 paper makes this confession: "How the brain stores and retrieves memories is an important unsolved problem in neuroscience."

Postscript: A 2022 paper has the very unjustified title "CaMKII: a central molecular organizer of synaptic plasticity, learning and memory." No robust evidence is produced for such claims, and we mainly have lots of uses of "may," "might," "perhaps" and "could." 

For example, here are the paper's uses of "may":

"CaMKII may exist in distinct populations in dendritic spines....CaMKII may serve as a ‘sponge’ to sequester various postsynaptic proteins, thereby triggering Ca2+-dependent trafficking of various proteins...Phosphorylation of SHANK3 by CaMKII may play a part here...This pool may represent cytosolic, unbound CaMKII molecules.... The interaction of CaMKIIα with α-actinin may also contribute to its interaction with F-actin...Reciprocal activation within a kinase–effector complex may be a general mechanism to maintain local CaMKII signalling for an extended period...This so-called inverse tagging of non-stimulated spines with ARC may increase the contrast of synaptic weights...CaV1.2-mediated influx may be sufficient to enable temporary activation of CaMKII...CaMKII may mediate LTP partly by phosphorylating TARPs...NMDAR-mediated calcium influx may make TARPs more accessible for CaMKII,...RHOA activation in response to glutamate uncaging may require other calcium-dependent processes in addition to CaMKII, which may indirectly regulate RHOA...RHOA may destabilize spines so that they can undergo structural changes during synaptic plasticity...Calcium signalling may be inhibited by CaMKII activation."

Here is where the paper uses the word "might":

"The CaMKII pools in spines that mediate these effects might be small and functionally defined by prolonged interactions of CaMKII with its various binding partners that enable them to contribute to the maintenance of basal transmission and long-term memory...There might be about 100-fold more CaMKII molecules in spines than GluN2B... LLPS of CaMKII might mediate not only the accumulation of CaMKII beneath the synaptic contact but also the formation of glutamate receptor nanodomains at the surface...That α-actinin also binds CaMKII might be important for the CaMKII mediated phosphorylation of S73 of PSD95...This might impair the inhibitory activity of the other helix in the dimer in trans, and thus facilitate substrate binding...CaMKII might need to maintain its own phosphorylation of T286 for continued interactions with other postsynaptic proteins... Synapses in a knockout neuron could be at a collective disadvantage and ‘lose out’ to other synapses formed nearby that might become stronger because resources of the presynaptic input neurons might be allocated to the synapses that they form with surrounding neurons....NMDAR-anchored CaMKII might phosphorylate nearby AMPARs that then become trapped when diffusing through AMPAR nanodomains...S831 phosphorylation augments single-channel conductance of AMPARs134,135, which might contribute to an increase in postsynaptic response during LTP induction."

Here is where the paper uses the word "could":

"It could be explained by an additional phosphorylation state or association with other proteins that protect CaMKII from phosphatase action..... These changes could occur at the sites of pre-existing CaMKII–SHANK3 complexes or could induce a redistribution of CaMKII from the spine interior to the PSD...Binding could provide a pool of CaMKII inside spines that can relocate moderately quickly during early phases of LTP... The kinase could be fully activated by Ca2+–CaM, resulting in increased EPSC amplitude....Other sources of calcium could drive CaMKII activation under basal, non-stimulated conditions to augment synaptic strength...This requirement for catalytic activity to increase AMPAR-mediated currents could reflect the need to phosphorylate other substrates... This increase in postsynaptic response could be mediated by recruitment of GluA1 homomeric AMPARs....A lasting increase in postsynaptic AMPAR function could be through phosphorylation of the auxiliary AMPAR subunit TARPγ2...That TTPL is not required for (non-fusion) TARPγ8 to localize AMPARs153 could be explained by a second, electrostatic interaction site between TARPs and the first PDZ of PSD95.... The phosphorylation of T305 and T306 reduces CaMKII–NMDAR binding157 and increases autonomous CaMKII activity, which could especially apply to phosphorylation sites in CaMKII target proteins that are important for LTD.'

Here is where the paper uses the words "hypothesized," "postulate," "perhaps" or "proposed":

"We postulate that the LLPS of CaMKII has two key roles in synaptic plasticity....It has been proposed that CaMKII acts to a large degree as an activity-dependent structural protein... The GluN2B–CaMKII interaction has been hypothesized to occur in a binding pocket different from the substrate-binding pocket...Such protein–protein interactions have been proposed to provide another mechanism for molecular memory during LTP....Early studies proposed that calcium–calmodulin (CaM)-dependent kinase II (CaMKII) has two discrete binding sites:....Most of this integration over seconds is perhaps due to the autonomous activity of CaMKII...Perhaps under basal neuronal-activity conditions, NMDAR-mediated calcium influx is more effective than CaV1.2-mediated influx in stimulating T305/T306 phosphorylation and thus preventing an increase in AMPAR activity....Perhaps CaMKII facilitates synaptic strengthening through trans-synaptic mechanisms...Perhaps the C terminus of GluA1-fused TARPγ8 has a higher propensity than the free TARPγ8 to detach from the plasma membrane and thus to bind to PSD95, independent of its CaMKII-mediated phosphorylation."