Crude "Finger in the Sand" Diagrams of "Engrams" Suggest Vacuous Theorizing

 There's a year 2025 paper on the Cornell physics paper server, one entitled "Engram Memory Encoding and Retrieval: A Neurocomputational Perspective." The author attempts to persuade us that he understands something about engrams (alleged memories stored in brains), something for which there is no real evidence. What we have in the paper is misstatements, hand-waving, bluffing and boasting, adorned by about the most primitive diagrams anyone could give. The "finger in the sand" crudity of the diagrams suggests that there is no real underlying understanding of how a brain could store or retrieve memories. 

Before discussing how crude are the diagrams, let me list some of the bad misstatements and half truths in the paper:

• The author states, "Despite substantial research into the biological basis of memory, the precise mechanisms by which experiences are encoded, stored, and retrieved in the brain remain incompletely understood." The truth is that scientists have no understanding at all of such a thing, and no robust evidence that any such mechanisms even exist. 
• The author states, " A growing body of evidence supports the engram theory, which posits that sparse populations of neurons undergo lasting physical and biochemical changes to support long-term memory."  This is false. The claimed evidence for engrams is all junk-science research guilty of sins such as way-too-small study group sizes and unreliable measurement techniques such as judgments of claimed "freezing behavior." 
• The author states, "These findings suggest that memory efficiency, capacity, and stability emerge from the interaction of plasticity and sparsity constraints." This is an example of vacuous hand-waving.
• The author states, "Modern discoveries of 'silent engrams' — which exist as physical traces but cannot be retrieved by natural cues, yet can be artificially reactivated — directly align with Semon’s concept of 'primarily latent modifications.' " There has been no actual discovery of 'silent engrams' or any other type of engram. All claims to have made such a discovery are unfounded, and not supported by any well-designed studies with high statistical power. 
• The author states, "Modern technological advancements have revolutionized the study of engrams, enabling researchers to investigate how specific memories translate into neuronal changes with unprecedented resolution (Luis & Ryan, 2022). These technologies include transgenic manipulation, optogenetics, chemogenetics, electrophysiology, and sophisticated behavioral techniques." The statement is untrue. Fancy technologies are used in studies looking for engrams, often as a kind of window-dressing to impress the easily impressed. But such studies have produced no robust evidence for any such thing as an engram. No one has ever found the slightest trace of any learned information in brain tissue by studying human brain tissue. Studies looking for evidence of engrams in animals have been a cesspool of junk science, and have been almost invariably guilty of very bad research practices such as way-too-small study group sizes, a lack of a blinding protocol, a lack of pre-registration, and the use of unreliable measurement techniques such as "freezing behavior" judgments. 
• The author states, "Modern neuroscience, armed with advanced technologies like optogenetics and immediate early gene labeling, has provided compelling evidence for the existence and dynamic nature of engram neurons and their ensembles." To the contrary, no such evidence has ever been produced. Any papers claiming to have produced such evidence will not hold up to critical scrutiny. 
• The author states, "Furthermore, the activity of engram neurons can be tracked in vivo during their maturation from encoding through consolidation using functional indicators like GCaMP (calcium indicators; Cupollilo et al., 2025). These experimental manipulations, particularly in the hippocampus, have demonstrated the necessity and sufficiency of engram cells for memory functions, enabling selective memory erasure, artificial recall, and even the creation of synthetic memories."  The first reference is one of many references the author makes to the paper "Early changes in the properties of CA3 engram cells explored with a novel viral tool" authored by Cupollilo and others, which is a very low-quality junk science paper using way-too-small study group sizes such as about 5 mice per study group, a paper guilty of defects such as failing to do any sample size calculation, and relying on unreliable "freezing behavior" judgments. The second sentence (beginning with "these experimental manipulations") is simply untrue, and none of the things claimed as "demonstrated" has actually been demonstrated. 

When the paper's author (Daniel Szelogowski) gives us a diagram regarding these claimed "engrams," we get a visual sign of the lack of any substantive theory underlying his claims. Below is a screen shot from the paper showing its Figure 1:

Notice the "finger in the sand" nature of the diagrams. The diagrams are like those a five-year-old child might draw, using crayons. When people understand things, they may produce very detailed diagrams showing the depth of their understanding. For example, do a Google image search for "genetic code" and you will get a very detailed diagram showing the exact scheme of representations used by DNA. But when people do not understand things, and they are merely feigning understanding, they may tend to produce very crude "finger in the sand" diagrams like those in the visual above. 

For example, imagine you had no understanding of how the Apollo 11 mission was able to leave our planet, land on the moon, and return to our planet. Rather than producing detailed diagrams showing things like the Saturn 5 rocket and the Lunar Excursion Module (LEM), you might produce "finger in the sand" type of diagrams like the ones below:

The Apollo 11 diagram above is as laughable a "finger in the sand" diagram as the diagrams in Szelogowski's paper. Neither Szelogowski nor any scientist has any real understanding of how a brain could ever encode and store any of the types of learned information that humans can remember. Neither Szelogowski nor any scientist has any real understanding of how a brain could ever instantly retrieve the correct information when a person hears a name or sees a face. 

When attempting to persuade us that they have some understanding of how memory could work in a brain, what those such as Szelogowski do is to mainly engage in vacuous jargon-adorned hand-waving.  Some vague wooly phrase such as "synapse strengthening" is used. Then some mentions are made of some type of actual chemistry observed in the brain, to make such vacuous hand-waving sound more substantive. There is no substance involved and no detail involved when Szelogowski states this:

"Synaptic changes primarily encode the specific content of a memory by modifying the strength of connections between neurons, while intrinsic and non-synaptic changes modulate the overall responsiveness and participation of individual neurons within the engram. This coordinated interplay ensures both the precise encoding of information and the dynamic integration of neurons into stable memory circuits."  

The claim above make no sense. Information is not encoded by some "strengthening" action. Humans are familiar with various ways in which information is encoded and stored, and none of these ways occur by strengthening.  When information is encoded and stored, what occurs is writing, according to some scheme of representation such as the English alphabet, the ASCII code, and so forth. 

For the neuroscientist, the problem is that nothing in the brain bears any resemblance to a some unit for writing information. So what do you do if you are a neuroscientist trying to suggest that brains write memories?  You appeal to "strengthening." and hope that people don't recognize how silly your language is. It's rather like a suitor who has no evidence that he is earning money, and who tries to impress a woman by bragging about how he is improving his muscles by weight training, while hoping that the woman somehow thinks that this is something like earning money. 

When people understand something and are asked to explain it, they tend to speak exactly in ways that show their understanding. Imagine you interview someone for a job as a computer programmer, and you ask the person, "How can I modify my web site so that it can store and remember data the users type in on a registration page?" If the job candidate is knowledgeable about this topic, he would tend to give a very exact and very detailed answer rather like this:

"Well, it depends on how much you want to spend, and how many people use your site.  If you don't have many users or don't want to spend much, you could use a simple pipe-delimited text file to store your data. Each row in such a file would give data on one user, and the pipe character would be used to separate the data fields such as name and email address. But finding a user in such a file requires a scan of the whole file which isn't efficient if you have many thousands of users. If you have many thousands of users, it might be better to use a relational database product such as MySQL. You could create a database, and then use the 'CREATE TABLE' command to create a new table with text storage fields such as UserName and Email. Once you had that table, you could have your web site add a new record for each new user, using the handy INSERT command available in SQL products such as MySQL. For the case of updating an existing user's data, you could use the UPDATE command available in SQL products such as MySQL. Products such as that take care of such details as converting from text strings to ASCII, and converting from ASCII to binary -- that's all encapsulated under the engine of such  relational database products. Your evocation of MySQL commands would take place in a handler function you would write that would respond to the press of a Submit button on your web site's form. Of course, some prefer never to get involved with SQL commands. If you're that type, there are various class libraries that will encapsulate all the SQL commands, so you don't have to remember any. Then you can just call the methods of some object that you have instantiated, and supply the data as arguments to a method of some class, a function that would take parameter inputs." 

But imagine you are interviewing a job candidate who does not know how a web page stores data. If you ask him how you can modify your web site to store user's data that they submit on a form, you might get some answer like this:

"Data processing is a very important function of a web site. Of course, when user's submit data, they want it to be saved not forgotten. Various components can be crafted that enable this functionality. It would require strengthening of the code that underlies your web site. It would require an encoding of information and a coordinated interplay between complex electronic components, as well as the participation of diverse units of functionality."

This job candidate apparently knows nothing about how a web site can store data a user types into a form. All he has given is some vacuous wooly phrases lacking in specifics. His answer sounds like the equally empty and vacuous lines I quote above from Szelogowski, who uses empty verbiage such as "coordinated interplay" and "modulate the overall responsiveness." Szelogowski sounds just as if he has no actual understanding of how a brain could store or retrieve a memory. And he's in the same boat as every neuroscientist, none of whom understand any such thing. 

One huge problem is that what Szelogowski is appealing to (synapse strengthening) is a slow process requiring hours or days. But that cannot explain human learning, which can occur instantly. If someone tells you that your mother or child has just died, you do not require hours or days to learn such a fact. You learn such a fact instantly. 

 Szelogowski's only mention of this issue is a feeble one. Appealing to some wild speculation, he says, "Furthermore, non-synaptic plasticity, such as the regulation of neural membrane properties, can operate on faster timescales, potentially enabling rapid initial information storage, complementing the slower, more enduring synaptic plasticity processes (Ferrand et al., 2025)." This is basically equivalent to a goofy statement such as, "I say memory storage occurs to synapse strengthening, but that isn't fast enough, so maybe there might be something else that is fast enough." 

Szelogowski's Figure 2 in the paper is just as vacuous a "finger in the sand" affair as his Figure 1. Below is his Figure 2:

This is not the kind of diagrams that people produce when they understand something.  A group of connected nodes as we see above is not even a sensible depiction of any such thing as the encoding of learned information. 

Just as unimpressive is Szelogowski's Figure 6. He takes a pentagram of circles, and repeats that pentagram about 13 times, with variations of how the circles are colored. It's another very crude "finger in the sand" kind of diagram suggesting that Szelogowski has no substantive understanding of how a brain could store a memory or preserve a memory for a lifetime or instantly retrieve a memory. 

Were anyone to ever explain how a brain could store memories and allow for instant memory retrieval, they would have to pay very much attention to speed. One of the biggest reasons why a brain cannot be the storage place of human memories is that humans can remember just the right information instantly, upon seeing a face or hearing a name. But there is nothing in a brain that can account for such blazing speed. We know the type of things that make possible fast retrieval in products humans make: things such as addresses, sorting and indexes. The brain has no addresses, no sorting and no indexes. So when a human instantly recalls many relevant facts after hearing a single name such as "Obama" or "Napoleon,"  that cannot be the result of brain activity. 

In this regard Szelogowski fails entirely. His paper makes zero uses of the word "speed," and has zero substantive references to the topic of  speed. The paper fails to even explain how so small an item as the word "cat" could be converted to some neuron state or synapse state. 

But think for a moment of how utterly impossible it could be to explain how a brain could encode (translate into neural and synapse states) all the types of things humans can learn and remember, which includes all of these types of things:

• Memories of daily experiences, such as what you were doing on some day
• Facts you learned in school, such as the fact that Lincoln was shot at Ford's Theater
• Sequences of numbers such as your social security number
• Sequences of words, such as the dialog an actor has to recite in a play
• Sequences of musical notes, such as the notes an opera singer has to sing
• Abstract concepts that you have learned
• Memories of particular non-visual sensations such as sounds, food tastes, smells, pain, and physical pleasure
• Memories of how to do physical things, such as how to ride a bicycle
• Memories of how you felt at emotional moments of your life
• Rules and principles, such as “look both ways before crossing the street”
• Memories of visual information, such as what a particular person's face looks like

Below are some quotes:

• "There is no such thing as encoding a perception...There is no such thing as a neural code...Nothing that one might find in the brain could possibly be a representation of the fact that one was told that Hastings was fought in 1066." -- M. R.  Bennett, Professor of Physiology at the University of Sydney (link).
• "No sense has been given to the idea of encoding or representing factual information in the neurons and synapses of the brain." -- M. R. Bennett, Professor of Physiology at the University of Sydney (link).
• "How the brain stores and retrieves memories is an important unsolved problem in neuroscience." --Achint Kumar, "A Model For Hierarchical Memory Storage in Piriform Cortex." 
• "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."  -- Two scientists, "Understanding the physical basis of memory: Molecular mechanisms of the engram."
• "There is no chain of reasonable inferences by means of which our present, albeit highly imperfect, view of the functional organization of the brain can be reconciled with the possibility of its acquiring, storing and retrieving nervous information by encoding such information in molecules of nucleic acid or protein." -- Molecular geneticist G. S. Stent, quoted in the paper here. 
• "Up to this point, we still don’t understand how we maintain memories in our brains for up to our entire lifetimes.”  --neuroscientist Sakina Palida.
• "The available evidence makes it extremely unlikely that synapses are the site of long-term memory storage for representational content (i.e., memory for 'facts'’ about quantities like space, time, and number)." --Samuel J. Gershman,  "The molecular memory code and synaptic plasticity: A synthesis."
• "Synapses are signal conductors, not symbols. They do not stand for anything. They convey information bearing signals between neurons, but they do not themselves convey information forward in time, as does, for example, a gene or a register in computer memory. No specifiable fact about the animal’s experience can be read off from the synapses that have been altered by that experience.” -- Two scientists, "Locating the engram: Should we look for plastic synapses or information- storing molecules?
• " If I wanted to transfer my memories into a machine, I would need to know what my memories are made of. But nobody knows." -- neuroscientist Guillaume Thierry (link). 
• "While a lot of studies have focused on memory processes such as memory consolidation and retrieval, very little is known about memory storage" -- scientific paper (link).

NSF Funding Search Suggests Neuroscientists May Scarcely Believe in Engrams

 How can you determine how seriously scientists believe in something? There are several ways. One way is to look for how much a particular thing is mentioned in articles and papers written by scientists. But that method may not be very reliable, because of sociological effects involving conformity. Within some scientific community, it may become a speech custom to assert the existence of something, even though scientists may not believe very strongly in such a thing. 

Another way to try to judge how seriously scientists believe in something is to look for opinion polls taken of scientists.  But scientists are very bad about reliably polling themselves about what they think. Opinion polls of what scientists believe are not very often done. When such polls are done, they are usually done poorly. Often the polls will be biased polls that do not offer a fair selection of choices, but offer a choice between some "orthodox" position and a negatively worded "straw man" version of an alternative position. For example, a scientist polled about evolution may be given a choice between believing in the least objectionable statement of evolution ("change over time") versus the least defensible contrarian position. So, for example, the question may ask:

Which do you believe

(A) That mankind evolved over time, or 

(B) That mankind was created about 6000 years ago as described in the Bible?

A more fair way to ask such a question would be to pose the question like this:

Please choose one of these answers:

(1) The human species arose by unguided natural processes.

(2) The human species arose because some higher power wanted humanity to exist. 

(3) I don't know how the human species originated. 

Another problem with polls of scientists is that they are rarely secret ballot polls.  If a poll is not a secret ballot poll, a scientist may be unlikely to answer it in any way that he thinks is against the majority opinion of scientists, for fear that he may "get into trouble" by answering in such a way. 

Then there is an entirely different way to judge what scientists believe and how strongly they believe in it. That way is to search for what is being funded. Scientists largely control their own funding. Federal agencies such as the National Science Foundation are given budgets, and committees of scientists decide whether particular requests for research funding are approved. If scientists believe strongly in some thing that can be scientifically investigated, they will tend to approve funding to either prove or further investigate that thing. As a general rule, the more funding they approve, the more strongly they believe in such a thing. 

The web page here allows you to search grants that have been approved by the National Science Foundation:

If you type in "cancer" as the search string, and press the Search button, you will get about 740 results.  By multiplying the part of the page showing results per page by the part of the page showing how many pages of results were returned, you can figure out the total number of results. For example, in the search result below, we have 30 results per page, and 25 pages of results. So apparently there are about 750 National Science Foundation projects that have some involvement with cancer:

Now, let's try a different search. We will look for funded research projects relating to dark matter, a hypothetical type of matter that has never been directly observed. Below is what the search term "dark matter" produces:

We get 59 pages of results, with about 30 results per page. The listed number of results is 1769. So apparently the National Science Foundation is funding about 1770 projects involving dark matter. I could write a separate post complaining about all of the money that is being wasted on such a search. But here I use this example simply to show that even when something has never been directly observed, scientists can believe in it very strongly. It seems from these results that many scientists really do believe strongly in the existence of dark matter. 

Now, let's try a different search. We will look for funded research projects trying to look for proof or evidence that memories are stored in the human brain. The term scientists use to mean a hypothetical spot in the brain where a memory is stored (or some set of brain components believed to be storing a memory) is the term "engram." When that term is used in the NSF grant search tool, we get the result shown below. 

There are only 11 results returned by the query, and they are all shown above. Unlike the query about research projects involving dark matter, which produced 59 pages of result, the query about research projects involving engrams produces only a single page of results, consisting of the 11 rows shown above. 

Four of these projects are not actually neuroscience projects, but instead computer science projects. Four of the rows refer to different project grants for a project called "Understanding memory in neuronal networks through a brain-inspired spin-based artificial intelligence." One of the projects ("Ice Regime Shifts of Arctic Lakes Drive Interactions and Feedbacks with Permafrost and Climate") only appears in the search results because it mentions someone with a last name of "Engram." So in terms of neuroscience projects involving the brain and attempts to find evidence for engrams, there are only six  funded projects. 

This is a very low level of funding for the concept of engrams. We may reasonably suspect from such results that perhaps neuroscientists do not even strongly believe in the idea of engrams. Maybe when neuroscientists refer to engrams or claim that memories are stored in brains, they are mainly "paying lip service" to some old idea they do not very strongly believe in. Or maybe neuroscientists have very little confidence in the idea that there can ever occur any discovery of memories stored in brains.

Let's look at the six neuroscience projects that came up in this query. 

• Project #2422939: Building a Conceptual Ecology of the Engram. This is a project allocated $208,090. The abstract of the project is laughable, because there are question marks spread all over it, in appropriate places, as if the writer was ridiculously careless. For example, we read this: "Finding the engram ? the neural mechanism of memory retention ? has been a guiding project for neuroscience since its earliest days. But while it has long been assumed that there was an engram, only recently with the development of new tools and technologies have specific engrams been identified and activated." That is not at all correct -- there is no robust evidence that engrams have been identified or activated. The project calls itself a "project in the philosophy of neuroscience." We can classify this as some kind of philosophy project rather than a real neuroscience research project. 
• Project # 2337788: A Molecular Pursuit for the Engram: Microfluidic temporal transcriptomics for single cell learning  This is a project allocated $300,000. This project is a real neuroscience project, one that is trying to prove a hypothesis that has little support among neuroscientists -- the hypothesis that "RNA encodes memory and learning in single cells." The abstract claims that "studies have shown that RNA holds information that can transfer memories between organisms in multicellular species like C. elegans, Aplysia, flatworms, rats, and fish, challenging a purely synaptic view." We have no mention of specific scientific papers, and the claim is not well-established. It sounds like this project is not one that will involve human memory, and that the scientists will try to show some type of information transfer in animals, something that the scientists might describe as "memory transfer." The project was started in November, 2023, and it has an end date of October 31, 2025. A search for the recent papers of the principal investigator (Saad Bhamla) seems to show no hopeful signs that this project is producing important results. 
• Project 2143910:  Reward Learning Shapes the Fear Circuit. This is a project awarded about $504,000, with a "total intended award amount" of $1,250,939. The project started in 2022, and has an "estimated completion date" of mid-2024. The abstract starts out by claiming "neuroscience research tends to conceptualize particular brain regions as specialized to encode particular types of memories," but the truth is that neuroscientists lack any understanding of how any part of the brain could encode a memory. The project seemed to be something about challenging existing guesses about which part of the brain encodes a particular memory.  The project seems to be finished, and failed to show any evidence for engrams. Unlike the next project mentioned below, the page for this project lists no publications that resulted from the project. 
• Project 1845355: Opposing roles of cortical input to dorsal striatum.  We have a project awarded $900,000, spread over 2019 to 2023. The project specification makes no mention of the word "engram." The only reason this project has shown up in the search results is that it is supposedly related to a paper "FosGFP expression does not capture a sensory learning-related engram in superficial layers of mouse barrel cortex." which apparently reports a failure to find an engram. 
• Project 1743392: Dendritic spine mechano-biology and the process of memory formation. This project was awarded nearly a million dollars. It started in 2017 and ended in 2023. We read, "This research project quantitatively characterizes the relevant molecular processes involved in the dynamical 'tectonic' reorganization inside a dendritic spine involved in forming memories." There is no actual evidence that dendritic spines have anything to do with memory. Tiny bumps on dendrites, dendritic spines look nothing something that could store information. Also, dendritic spines are too unstable and short-lived to be a storage place for memories that can last for decades. We have a list of papers that resulted from the project. None of them sound like anything having much relevance to the topic of engrams or memory storage, except for the paper "Exploring the F-actin/CPEB3 interaction and its possible role in the molecular mechanism of long-term memory,"  which you can read here. Early on that paper states, "The growth and stabilization of dendritic spines is thought to be essential for maintaining long-term memory."  No, the tiny stubs that are dendritic spines bear no resemblance to an information storage device, and dendritic spines are too short-lived and unstable to be something that can explain memories that can last for decades. The paper gives us no observations supporting the claim that dendritic spines have anything to do with memory. Instead it merely provides a " computational structural model of the F-actin/CPEB3-ABD complex." The million dollars spent on this project did nothing to show any neural basis for memory, and did nothing to establish the existence of engrams in the brain. 
• "Project 8809208: Functional Dissociation Within the Hippocampal Formation: Learning and Memory."  This is a project completed in 1992. It was granted $163,070. We have no mention of any publications that resulted from the research. 

There is one other NSF-funded project I am aware of that is related to a search for engrams.  $600,000 has been allocated for the project described on this page:

https://www.nsf.gov/awardsearch/showAward?AWD_ID=2050850&HistoricalAwards=false

The project (NSF award # 2050850) is one entitled "Elucidation of RNA-Based Mechanisms of Long-Term Memory Storage." The idea of an RNA-based mechanism of long-term memory storage is an absurd one. RNA is a short-lived molecule. Referring to David Glanzman, the project incorrectly states, " the principal investigator has discovered that long-term memory (LTM) in the marine snail Aplysia appears to be stored in neurons by nuclear changes." No such thing has been discovered by Glanzman or anyone else. Glanzman's paper here received lots of press incorrectly talking about a "memory transfer" between marine snails.  The paper provided no robust evidence for any such thing, and involved study group sizes of only 7, way too small for a reliable result. A search for David Glanzman's recent papers on Google scholar shows that the NSF award # 2050850 has failed to produce any interesting papers backing up claims of RNA-based mechanisms of long-term memory storage. 

Then there is NIH Project # 1DP2MH129985-01 discussed on this page. Having funding of $1,434,188, the project had a title of "The Epigenetic Encoding of Learning and Memory." The project had an end date in 2024, but it did not produce any papers backing up the idea of memory storage in the epigenome, or anywhere else in the brain.. 

On the same official project page, there is a Publications section that lists 7 publications that resulted from this project (there is a double-listing for one of them). None of them do anything to establish the "epigenetic encoding of learning and memory" mentioned in the project title.  The papers are these:

• "Control of striatal circuit development by the chromatin regulator Zswim6" (link). This paper makes no mention of memory or learning. 
• "Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory" (link). The study provided no good evidence to back up its claim that H2BE has any relation to memory. To test the claim, the study produced "H2BE knockout" mice, whose performance was compared to normal test mice. The first test used was a "novel object recognition" test that is not an effective way of judging animal memory when a blinding protocol is not followed. In the test scientists attempted to judge how much time a mouse spends exploring a type of object it has already been exposed to, using manual scoring -- we are told "Time spent interacting with each object was manually analyzed." Such a test is not a reliable way of judging memory in rodents whenever there is a failure to follow a blinding protocol, and no mention is made that a blinding protocol was followed. The second test used was a test requiring a judgment of "freezing behavior," and such tests are utterly reliable in judging whether an animal recalled, for reasons discussed at length here. 
• "A nociceptive amygdala-striatal pathway for chronic pain aversion" (link). No mention is made of learning or memory in this paper. 
• "Loss of DOT1L function disrupts neuronal transcription, animal behavior, and leads to a novel neurodevelopmental disorder" (link). The authors first discuss 11 humans who had variations in something called DOT1L The paper claims that 2 of these 11 had "intellectual disability" without giving us any specifics. This does not constitute any evidence of a relation between this DOT1L and memory. The paper also claims that DOT1L modification in zebrafish had some effect on their cognitive performance. But the claim has no clear reference to memory, and the claim is not demonstrated, because the number of zebrafish tested is way too small, being only 3 zebrafish. There is then a claim that DOT1L modifications have some effect on mice. But no clear claim is made of an effect on memory performance. 
• "Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling" (link). The research discussed does not involve learning or memory. 
• "SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry" (link). The research discussed does not involve learning or memory. 
• "Identification of a transcriptional signature found in multiple models of ASD and related disorders" (link). The research discussed does not involve learning or memory. It merely makes a passing reference to memory, claiming (without providing any specifics) that a "histone code" plays a role in memory.

These are all the papers I am able to find searching for research on "engrams" funded by the National Science Foundation (I have added a couple of other projects I knew of that could have appeared in such a search if the word "engram" had appeared in their abstracts). Although adding up to a total funding of several million dollars, the funding is relatively little, compared to the money spent on other things scientists believe in, such as dark matter. The number of projects looking for proof of engrams is small, with only a tiny number of scientists doing such research. 

It's rather as if deep down inside, neuroscientists scarcely even believe in engrams, or as if deep down inside, neuroscientists know that any project looking for proof of engrams will be extremely unlikely to succeed.  Maybe some part of their minds have figured out that if it was really true that brains stored memories, microscopes would have discovered proof of that decades ago. 

The decisions scientists make about what to fund is a factor speaking in a louder voice than what scientists claim about what scientists believe. The weak funding scientists have given to searches for proof of engrams may suggest that neuroscientists do not really have high confidence in the idea that memories are stored in brains. The weak results of the small number of projects related to claims of brain storage of memories (engrams) suggest that research into this area is futile in terms of substantiating claims of a brain storage of memories. 

No, They Didn't Find in a Brain "3 Copies of Every Memory," and They Never Even Found One

In my post "Why the Academia Cyberspace Profit Complex Keeps Giving Misleading Brain Research Reports" I discussed the economic reasons why we keep getting misleading research about brains, and misleading headlines about brain research. The analysis in that post holds true not just for brain research, but for scientific research in general. We live in an economy in which misleading stories about scientific research and groundless but interesting-sounding scientific speculation are highly incentivized. To give a short synopsis of what I discussed at much greater length in that post, the economic motivations are like this:

(1) Scientists are judged by how many papers they publish and how many citations such papers get.

(2) Because of publication bias (in which papers reporting positive results and particularly interesting-sounding positive results are more likely to be published), scientists are strongly motivated to publish papers claiming positive results and also claiming interesting-sounding results.

(3) Wishing to make themselves appear like sources of important research breakthroughs to help justify their exorbitant tuition, universities are motivated to produce press releases exaggerating the importance of research papers published by their professors.

(4) Since science news is published on web pages with ads that generate revenue for the people running or funding the web pages, with revenue proportional to how interesting-sounding a story is, those running science news web sites or science analysis web sites have an enormous economic motivation to create clickbait headlines that generate higher numbers of page views, and more advertising revenue. Science news sites these days are almost always built in the form of headlines that you must click to read the story, and each time this causes a web page with ads to appear, the people running or funding the site get money from views of the ads displayed on the page you opened up.

The result of all of this is a very wacky world we might call the world of scitainment, to coin a word that combines the words "science" and "entertainment." Scitainment is a part of the internet that blends science and entertainment. Very much of what we read in this strange world of scitainment is true, and very much of it is false. The world of scitainment blends fact and fantasy, always trying its best to produce entertaining stories and clickbait headlines. It's all about luring you in to click on the stories, so that you go to pages that generate ad revenue for the people running the web sites. 

One of the web sites involved in pushing scitainment is the ad-heavy site www.livescience.com, where we have many science headlines that simply are not true. To give some examples:

• On the Livescience site we had the utterly untrue headline "Building blocks of life' discovered on Mars in 10 different rock samples." The story discusses some observations of biologically irrelevant chemicals on Mars, none of which are ingredients of life or building blocks on life.  
• The same Livescience site had an article claiming a woman was hit by a meteorite while drinking coffee outside, although a space.com story tells us no such thing happened. 

• A story at the LiveScience site was entitled " 'This might be the seeds of life': Organic matter found on asteroid Ryugu could explain where life on Earth came from." The story was rubbish for several reasons: (1) Scientists do not believe that life ever existed on the asteroid  Ryugu or on any other asteroid. (2) There is no scientific concept of any such thing as a "seed of life," in the sense of something causing life to arise from non-life (with the exception of plant seeds, and plant seeds were not found on Ryugu).  (3) No actual components of life were found on the asteroid Ryugu, and most organic molecules are not components of life. 

• Another story at the LiveScience site referred to a claimed discovery of the simplest amino acid (uracil) on an asteroid, in the faintest trace amount of only 13 parts per billion. The headline at the LiveScience site made the very untrue claim that this "could explain the origin of life." Living things require twenty types of amino acids, which must be massively arranged in very specially ordered arrangements to make many types of the very hard-to-achieve molecules called proteins.  The discovery of one type of amino acid in the faintest trace amounts no more explains the origin of life than the discovery of a twig on the ground (making the letter "I") explains the origin of books consisting of vey much well-constructed prose. 

• Another article on the LiveScience site was devoted to selling the groundless idea that there is a "dark mirror" universe inside ours. 

• Another article on the LiveScience site had the nutty title "The 1st life in the universe could have formed seconds after the Big Bang."  Anyone familiar with the incredibly high temperatures and density at such a time (preventing all chemistry and even the existence of atoms) should understand how crazy such a claim is. 

• Another article on the LiveScience site had the phony title "Here's what we learned about aliens in 2020," a reference to extraterrestrials. Of course, we did not learn anything about extraterrestrials in that year. 

• Another article on the LiveScience site had the phony title "These weird lumps of 'inflatons' could be the very first structures in the universe."  We saw a visual of some strange structure that looked like a planetary nebula. The caption read, "Shown here, one of the dense clumps of inflatons that emerged during the inflation phase of the Big Bang, in the infant universe."  The caption led the reader to believe he was looking at some photo of something in space.  But the photo was not a photo of anything observed in space.  It was merely a photo of some junk generated by an entirely speculative computer program. No actual "inflatons" have ever been observed, and the program was based on one of the innumerable speculative models of the unproven cosmic inflation theory.

As the examples above show, you should not assume a claim is true merely because you read a headline suggesting it is true at the LiveScience site at www.livescience.com.   The latest example of a misleading headline at the site is an article with the groundless headline "The brain stores at least 3 copies of every memory." Human beings recall things, but no scientist has ever discovered even one memory in a brain. 

You can pretty much figure out that the story is baloney the moment you read that the research discussed is merely research based on mice rather than humans.  Letting our imaginations run wild, we can imagine some investigator of human brain tissue confirming the claim that brains keep three different copies of each memory. For example, an investigator might keep scanning the brain of a dead person, and then announce something like, "I found the words 'the battle of Hastings occurred in 1066' in three different spots of the brain." But we can imagine no possible observations of mice brains that would ever justify the claim that a memory was stored in a mouse brain.  For example, a researcher could never announce that he found the words "mouse traps are dangerous" in some part of a mouse brain, simply because mice don't use language. 

Misspeaking both in its headline and in its text, the article says, "The scientists found that, in rodents, the brain stores at least three copies of a given memory, encoding it in multiple places in the organ." No, scientists found no such thing. The article refers to the junk-science paper "Divergent recruitment of developmentally defined neuronal ensembles supports memory dynamics." It is true that in the abstract of the paper the authors claim " we discovered that memory encoding resulted in the concurrent establishment of multiple memory traces in the mouse hippocampus."  But because the authors used very bad research practices, they provided not the slightest bit of robust evidence for such a claim. 

The paper is behind a paywall, but anyone can read a preprint of the paper that allows us to see the Questionable Research Practices that were used.  The defects are as follows:

(1) The study group sizes were way-too-small, consisting of groups such as only 4 mice or only 5 mice or only 8 mice or only 10 mice. No one should take seriously any experimental rodent research study using fewer than 15 rodents in each study group, and for most effect sizes a larger study group size such as 30 mice is needed. The authors would have discovered the inadequacy of their study group sizes if they had done a sample size calculation like good scientists, but they failed to do that. The paper "Prevalence of Mixed-methods Sampling Designs in Social Science Research" has a Table 2 giving recommendations for minimum study group sizes for different types of research. The minimum number of subjects for an experimental study is 21 subjects per study group. 

(2) We hear no discussion of the following of a detailed blinding protocol, something that would need to exist for a study like this to be taken seriously. The only mention of a blinding procedure is the mere remark that "To reduce potential bias in the analysis, the researcher conducting the analysis was blind to the experimental

group to which animals belonged until after the data analysis was completed."  When you are using very small study group sizes such as only 4 mice or only 8 mice, it is typically the case that mice can be recognized visually, meaning a researcher can tell things he was not told, such as whether a mouse was in a control group.  Serious use of a blinding protocol requires a careful protocol that would require at least a long paragraph to state, and we have no evidence of such a thing in this paper. 

(3) The experiment was thoroughly entangled with the use of a worthless technique for measuring memory recall in mice, the defective technique of trying to judge "freezing behavior" in mice.  The preprint paper uses the word "freezing" 77 times, to show how the experiments were thoroughly dependent upon the use of such a technique. All experimental neuroscience papers depending on such judgments of "freezing behavior" are junk science papers. 

"Freezing behavior" judgments work like this:

(1) A rodent is trained to fear some particular stimulus, such as a red-colored shock plate in his cage. 

(2)  At some later time (maybe days later) the same rodent is placed in a cage that has the stimulus that previously provoked fear (such as the shock plate). 

(3) Someone (or perhaps some software) attempts to judge what percent of a certain length of time (such as 30 seconds or 60 seconds) the rodent is immobile after being placed in the cage. Immobility of the rodent is interpreted as "freezing behavior" in which the rodent is "frozen in fear" because it remembered the fear-causing stimulus such as the shock plate. The percentage of time the rodent is immobile is interpreted as a measurement of how strongly the rodent remembers the fear stimulus. 

This is a ridiculously subjective and inaccurate way of measuring whether a rodent remembers the fear stimulus. There are numerous problems with this technique:

(1) There are two contradictory ways in which a rodent might physically respond after seeing something associated with fear: a flight response (in which the rodent attempts to escape) and a freezing response (in which the rodent freezes, not moving). It is all but impossible to disentangle which response is displayed when the rodent is presented with a fear stimulus. A rodent who remembers a fear stimulus might move around trying to escape the feared stimulus. But under the "freezing behavior" method, such movement would not be recorded as memory of the feared stimulus, even though the fear stimulus was recalled. 

(2) Rodents often have hard-to-judge movement behavior that neither seems like immobility nor fleeing behavior, and it is subjective and unreliable to judge whether such movement is or is not "freezing behavior" or immobility. 

(3) Movement of a rodent in a cage may be largely random, and not a good indication of whether the rodent is afraid and whether the rodent is recalling some fear stimulus. 

(4) Rodents encountering a fear-provoking stimulus in human homes (such as a mouse hearing a human shriek) almost never display freezing behavior, and much more commonly display fleeing behavior. I lived in a New York City apartment for many years in which I would suddenly encounter mice, maybe about 10 times a year. I never once saw a mouse freeze when I shrieked upon seeing it, but invariably saw the mouse flee. 

(5) Freezing behavior in a rodent may  last for a mere instant, as in humans. So it may be extremely fallacious to do something such as trying to observe 30 seconds or 60 seconds of rodent movement or non-movement, and try to judge whether fear or recall occurred  by judging a "freezing percentage" over such an interval. Almost all of that time may be random behavior having nothing to do with fear in the rodent or memory recall in the rodent. 

For experiments not involving recall of a fearful stimulus, the Morris Water Maze test can be used to reliably measure recall in rodents. There are two reliable ways to measure fear recall in rodents. The first is to measure heart rate, which very dramatically spikes in rodents when they are afraid. The second is to measure an avoidance of a fearful stimulus.  The simple technique is illustrated in the visual below:

But instead of using such reliable techniques, our neuroscientists continue to use the very unreliable technique of trying to judge recall of fear-related memories in animals by making subjective judgments of "freezing behavior." Why would they continue to use so stupid and unreliable a technique? I can think of two reasons:

(1) Neuroscientists are People of Custom just like Roman Catholic priests are People of Custom. So neuroscientists may keep using some very old and ineffective technique as a matter of "clinging to the old custom," rather like the way Roman Catholic priests kept reciting the Mass in Latin very long after almost no one understood Latin. 

(2) Neuroscientists may prefer to use an unreliable technique for measuring fear-related memory recall in rodents, because using that bad technique increases the chance of them producing research papers that report invalid but interesting-sounding results consistent with "brains store memories" dogmas.  Similarly, if a researcher uses an unreliable technique for detecting heat traces in clouds, it will increase the chance that he can end up with some paper claiming to show heat blips in clouds that he may claim as evidence for extraterrestrial spaceships in the sky. The unreliable measurement technique is the best friend of the person trying to support untrue claims. 

Thoroughly dependent on a bad measurement technique for judging whether rodents recalled a fearful stimulus, and also involving way-too-small study group sizes such as only 4 or 5 rodents, the low-quality science paper "Divergent recruitment of developmentally defined neuronal ensembles supports memory dynamics" has provided zero robust evidence that there is a copy of a memory in any brain. No such robust evidence has ever been provided by neuroscientists. As discussed in my post here, the quickly-preserved brains of thousands of people have been thoroughly studied by different "brain bank" projects, and by microscopic examination no one ever found the slightest evidence of a memory stored in a brain. Never through microscopic examination of a brain has even a single piece of information as small and humble as "birds fly" or "dogs bark" or "Earth has a moon" ever been found. nor has anyone ever found in any brain by microscopic examination even the crudest or blurriest  image of anything anyone saw. 

Click on the image to read it better

Postscript:  When "freezing behavior" judgments are made, there are no standards in regard to how long a length of time an animal should be observed when recording a "freezing percentage"  (a percentage of time the animal was immobile). An experimenter can choose any length of time between 30 seconds and five minutes or more (even though it is senseless to assume rodents might "freeze in fear" for as long as a minute).  Neuroscience experiments typically fail to pre-register experimental methods, leaving experimenters free to make analysis choices "on the fly," after they have gathered data. So you can imagine how things might work. An experimenter might judge how much movement occurred during five minutes or ten minutes after a rodent was exposed to a fear stimulus. If a desired above-average amount of immobility (or a desired below-average amount of immobility) occurred over 30 seconds, then 30 seconds would be chosen as the interval to be used for a "freezing percentage" graph. Otherwise,  if a desired above-average amount of immobility (or a desired below-average amount of immobility) occurred over 60 seconds, then 60 seconds would be chosen as the interval to be used for a "freezing percentage" graph. Otherwise,  if a desired above-average amount of immobility (or a desired below-average amount of immobility) occurred over two minutes, then two minutes would be chosen as the interval to be used for a "freezing percentage" graph. And so on and so forth, up until five minutes or ten minutes. Such shenanigans drastically depart from good, honest, reliable experimental methods. 

The paper discussed above did not pre-register any methods, so after gathering data the experimenters were free to analyze the data in any way they pleased. Some of their "freezing behavior" graphs are made using a time interval of three minutes, and others are made using a time interval of five minutes. Genuine fear-freezing in an animal would be something lasting only a few seconds. The longer the interval of time used as a basis for a "freezing behavior" graph, the more unreliable freezing behavior judgments are as a measurement of fear recall. When an interval of longer than 30 seconds is used as the basis for a "freezing percentage" graph, then you have a particularly unreliable and particularly deplorable use of such a technique; and the longer the time interval is above 30 seconds, the more unreliable and deplorable are claims that such graphs are measurements of how well an animal recalled something. 

Exhibit B That Scientists Have No Understanding of a Physical Basis of Human Memory

 On this site I have published several posts with titles beginning with "Exhibit A" or "Exhibit B." Each such post examined an article or paper which prevented prima facie evidence that neuroscientists are lacking in one of the basic things they often claim to possess. The posts are these:

Exhibit A Suggesting Scientists Don't Understand How a Brain Could Store a Memory

Exhibit A Suggesting Scientists Don't Know How a Brain Could Retrieve a Memory

Exhibit B Suggesting Scientists Don't Know How a Brain Could Retrieve a Memory

Exhibit A Suggesting Scientists Have No Understanding of How a Brain Could Imagine Anything

Now let's look at another article or paper that offers this type of "Exhibit A": a 2021 paper by neuroscientist C. R. Gallistel entitled "The Physical Basis of Memory." The paper tells a "getting nowhere" story, and offers an excuse for the lack of progress: the extremely lame excuse that neuroscientists are too big fans of the 17th-century philosopher John Locke. The author states this: 

"The unbreakable embrace of Locke’s theory by neuroscientists explains why we have still not discovered the physical basis of memory, despite more than a century of efforts by many leading figures. Researchers searching for the physical basis of memory are looking for the wrong thing (the associative bond) in the wrong place (the synaptic junction), guided by an erroneous conception of what memory is and the role it plays in computation. That is the hole we have dug for ourselves."

No, actually you can usually get a neuroscience PhD without even taking an introductory course in philosophy, and neuroscientists have not tended to be either big followers of any philosopher or people very interested in philosophy. Referring to "the engram" (an imagined neural or synaptic storage place of memory), the author then makes tells us that " the role of memory as the transmission medium for the acquired facts that guide future behavior goes unmentioned in neurobiological reviews of the search for the engram (Poo et al., 2016; Tomonori, Duszkiewicz, & Morris, 2013)." Oops, it sounds like our neuroscientist memory theorists are dropping the ball. The author then claims that the neuroscience literature "documents beyond reasonable argument that brains contain facts." No, that is not true; we merely know that humans and animals learn facts, not that brains contain facts. 

The author offers this evidence for the claim that "the brain contains facts": the fact that the average English speaker knows 40,000 words and that "the cognitive science literature shows that we can remember thousands of drawings of objects and thousands of boring vacation slides and the even more boring target and distractor items in visual search experiments—objects and scenes and drawn objects that we have seen or felt or smelled only once for a few seconds or less seconds or less (Brady, Konkle, Alvarez, & Oliva, 2008; Hutmacher & Kuhbandner, 2018; Konkle, Brady, Alvarez, & Oliva, 2010; McGann, 2017; Shepard, 1967; Standing, 1973)."  That is merely evidence that humans can remember things, not that brains store what we remember. 

What some of these experiments show is that humans can form long-term memories of things seen for only a few seconds, things seen only a single time (something we need no experiments to prove, since this ability is a common fact of everyone's experience). Far from supporting claims that memories are stored in brains, such studies conflict with or clash with such claims. The ability of humans to instantly form new memories is something that no neuroscientist can credibly explain. Existing hand-waving speculation about "synapse strengthening" as a cause of memory formation are inconsistent with the ability of humans to instantly form new memories, because such synapse strengthening would require new protein synthesis taking many minutes. That's why you often hear neuroscientists make the ridiculous claim (contrary to every person's experience) that humans take minutes to create a new memory. 

The author then gives us a long paragraph discussing how humans and animals compute things. Why mention that in a paper entitled "The physical basis of memory"?  Maybe because no such physical basis is known, so if the "physical basis of memory" is your topic, you have to fill up your pages saying something.  On and on the author goes, talking at length about topics such as dead reckoning (a distance estimation ability) and other topics that have nothing to do with a physical storage of memory. 

After wandering around for several long paragraphs about mostly irrelevant topics, the author then fires another broadside against his fellow neuroscientists:

"In order to pass into and through a channel of communication, a message must be encoded (Shannon, 1948). Therefore, those of us pursuing the material basis of memory must ponder what the code might be and how it could be physically realized (Gallistel, 2017a, 2017b) This question about the memory code makes neuroscientists deeply uncomfortable, for which reason, it is never posed in the vast literature on the neurobiology of memory."

That's pretty much correct, although it might have been more fair to have said "almost never posed" than "never posed." It is easy to understand why neuroscientists virtually never make any attempt to suggest a possible encoding scheme by which a brain might physically store memories. The reason is that humans learn and remember so many different types of things that any such encoding scheme would have to be almost infinitely more complicated than the one known coding scheme used by the body (the genetic code by which triplets of nucleotide base pairs stand for particular amino acids).  If such an encoding scheme existed it would have to be some miracle of design more complex than any coding scheme humans have ever invented. It would be impossible to explain how such a coding scheme (capable of storing text using alphabets and musical notation schemes only a few thousand years old) could have naturally arisen by evolution. So neuroscientists pretty much ignore the whole problem of neural encoding. 

Our author rambles on and on, mostly on digressions that have nothing to do with how a brain could physically store a memory. In his second to last paragraph he claims that "polynucleotides" are "the only biological structures that are known to function as transmitters of information." But haven't we been told a thousand times that axons transmit sensory information to the brain from the eyes? Axons are not polynucleotides, but wire-like structures. In his last sentence the author dismisses the leading claim of neuroscientists about how a brain stores memories (the very vague idea of "synapse strengthening") and offers only the equally vague catchphrase of "information-bearing molecules" as an alternative. He states as his last sentence, "The material realization of the engram is probably not to be found in the synapse, much less in multi-neuron cell assemblies (the neural equivalent of Locke’s dust-ball concepts); it is to be found in information-bearing molecules inside neurons, operated on by molecular level computational machinery (Akhlaghpour, 2020)."

We end up with the author having presented no theory as to how there could be any physical basis of memory. All he's done is to make a lame excuse involving the claim that neuroscientists were too influenced by John Locke, and given us a link to some paper by Akhlaghpour. An examination of the paper by Akhlaghpour will leave you disappointed. 

The paper by Akhlaghpour is entitled "An RNA-Based Theory of Natural Universal Computation." Akhlaghpour is not a professor, but merely a post-doctoral fellow. The paper starts out very badly in its first paragraph by stating, "Some examples of computation in biology include: using vision to guide wing movement in insect flight, language acquisition in humans, decision ­making in single­ celled ciliates  [1,2], and embryonic development, the decisional process of beginning with a single cell and coordinating across daughter cells to produce a complex finely ­detailed three ­dimensional structure." No, language acquisition is not an example of computation, nor is embryonic development. A baby does not form by computation. Morphogenesis is an example of extremely complex physical three-dimensional organization and construction, which is not mere computation. The Merriam Webster dictionary defines computation as "the action of mathematical calculation" or "the use of computers, especially as a subject of research or study."

At the end of page 7 Akhlaghpour says, "I propose the theory that the non­protein­ coding portion of genome and transcriptome contains the data and programming material of an undiscovered universal computation system in biology." So vague an idea is best described as a hypothesis rather than a theory.  We then have the presentation of some extremely far-fetched speculations imagining that DNA or RNA might have all kinds of marvelous properties that no one has ever discovered in them. On page 16 these speculations go astray by trying to convince us that nucleic acids could have an addressing system. We read this:

"The method of nesting terms through RNA stem loops presents an opportunity to implement addressable memory

and variable substitution. One such implementation is illustrated in Fig 6. In this model, each variable is assigned

an address (specified by a unique sequence of nucleotides)."

DNA has been exhaustively analyzed, and no such thing has been found. There is no evidence of any addresses or addressable memory anywhere in DNA, RNA, or anywhere in the brain.  

On page 22 Akhlaghpour discusses what seems like a fatal difficulty for his theory:

"Another challenge for a solely RNA based molecular engram theory is RNA stability. If a molecule were to serve as a   memory   engram  it  must  at  least  exhibit  stability   over  similar   time  periods   as   cognitive   memories.   RNA molecules have an average half ­life of around 7 hours."

Nothing that he says extracts himself from this problem. He mentions the possibility of RNA storing data back into DNA. But that would be like a giant steel ball chained to the leg that would slow things to a crawl, preventing the instant memory recall we know occurs. 

On the same page Akhlaghpour attempts to convince us that his RNA scheme could be fast enough, stating this:

"Can RNA modifications occur fast enough to potentially facilitate cognition? Two of the most well­ studied RNA

processes are transcription and translation. RNA Polymerase II transcribes RNA molecules at a rate of 18­-100 nt/s

equivalent to 36­-200 bits/s [bits per second].  And the ribosome translates RNA to protein at a speed of roughly 5­11

aa/s equivalent to 30­-66 bits/s [bits per second]. It is difficult to quantify how fast animals think but studies of different

languages show that the information rate of human speech is roughly on the order of 40 bits/s (languages that

are   spoken   faster   have   lower   bits   per   syllable   than   languages   that   are   spoken   slower)....This means that RNA operations can in principle be fast enough to encode/transmit

ideas communicated in speech as single RNA molecules."

There are several things wrong here. First, the rate at which RNA can be translated to protein is irrelevant here, if we are imagining a memory is read from DNA. The relevant rate is the rate of transcription, the rate at which DNA is read to produce RNA. Akhlaghpour has overstated the speed of RNA transcription (reading DNA to produce RNA). The recent paper here lists the speed of RNA Polymerase II transcription as less than 4 kilobytes per minute, which is less than 67 bytes per second. Also it is not true that humans recall at only 40 bits per second. A slow old man like me can clearly sing the first four lines of Gilbert and Sullivan's "I Am the Very Model of a Modern Major General" song at a rate of 204 bytes in 7.5 seconds, which is a rate of 218 bits per second. That means people can recall things at a speed three times faster than the speed of RNA transcription just quoted. Even without considering the problem of "finding the right spot to read at," it turns out reading from DNA would be three times too slow to account for fast human memory recall.  So it is not true that " RNA operations can in principle be fast enough to encode/transmit ideas communicated in speech as single RNA molecules," as Akhlaghpour claims. 

But you must also consider that there is no sorting, no addresses and no indexes anywhere in the brain or DNA or RNA (contrary to the chimerical imaginative speculations of Akhlaghpour). That means trying to recall the correct answer when asked a question or asked to recite something (using brain memory storage) would proceed at a rate very many thousands of times slower than a rate of 67 bits per second,  because there would be the enormous "finding the needle in the haystack" speed delay of having to find exactly the right spot where a memory was stored in the brain or its DNA, and a brain would never know where that exact right spot was. 

Akhlaghpour is trying to make use of some abstract computer science notions of "universal computation" and a "Turing machine" that is built upon the idea of some machine that takes a line-like one-dimensional paper feed of  characters and produces output that is also a one-dimensional paper feed of characters, rather like a stock ticker.  Computer science calculations about such a machine are not applicable to a mind. Rather than receiving a single line of characters, a human mind simultaneously receives inputs from lots of different sources:

• visual input that is vastly more complex than just a one-dimensional stream of characters;
• auditory input;
• touch input from the hands;
• smell input;
• taste input;
• memory recall input.

And similarly, rather than producing any one-dimensional output such as a line-like stream of characters, mental activity can produce three-dimensional output such as the simultaneous singing, expressions and dancing of a Broadway performer. 

On the next page (page 23) Akhlaghpour makes the little confession that under the byzantine speculative scheme he is imagining, the mere addition of one number to another would require something like 10,000 operations.  But then on the same page he brags that his scheme is not evoking "implausible molecular processes." Such a boast is untrue, and the molecular processes evoked are utterly implausible and unworkable as any explanation for human memory performance. He notes that "current theories of synaptic plasticity and network activity cannot explain learning, memory, and cognition." 

Akhlaghpour's theory ends up being nothing that can explain memory.  His paper has mainly been busy trying to create some "castle in the clouds" theory of universal RNA computation that has nothing to do with explaining memory. As kind of a sideshow, he says a little related to explaining memory, but it's a half-hearted affair that does not nudge the giant rock of this Everest-sized problem. 

Human DNA has been exhaustively studied in all parts of the brain. Contrary to Akhlaghpour's theory:

• No one has ever found any evidence of human conceptual information (such as school-learned information) by studying brain tissue or DNA from brains.  
• No one has ever found any evidence of human episodic memories (such as images seen or sounds heard) by studying brain tissue or DNA from brains.  
• No one has ever found any sign of any addresses, indexing or sorting (or anything else that could explain instant human recall) in human brain tissue or DNA from brains.  
• Computing as occurs in computers requires things such as an operating system (an incredibly complex coordinated body of low-level software routines) and lots of application software. There is not the slightest sign of any such thing in the human brain. 
• No one has ever found any sign of any coding system or encoding system in human brain tissue or DNA from brains, except for the genetic code used by every cell in the human body.

Summarizing the paper of C. R. Gallistel entitled "The Physical Basis of Memory." we can say that it does very little but complain that current theories offer no credible physical theory of memory, and then ends up by giving a link to some speculative paper that also completely fails to offer any credible physical theory of memory. The excuse Gallistel gives for why scientists have found no physical basis for memory (that brain scientists were too big fans of John Locke) is a ridiculous-sounding excuse. A much better explanation is that scientists have got nowhere on the quest for a brain physical basis of memory simply because brains do not store memories. 

Memory must be something like a spiritual reality rather than a neural reality. It isn't true, as many think, that we have souls or spirits that come into play only during unusual psychic experiences or religious experiences.  Instead, the most basic processes of our minds such as thinking and insight and remembering must utilize human non-physical capabilities and abilities. We don't form new memories or recall answers at the very sluggish speed of brains; we acquire new memories and recall answers at the speed of souls.