Pre-discussion Tutorials for Topics Mentioned in From Bacteria to Bach and Back

Daniel Dennet, From Bacteria to Bach and Back: The Evolution of Minds, W.W. Norton & Company, 2017.

Dennett discusses a wide range of topics in this book, many of which I have some familiarity with due to my background as a working scientist (here is a link to my published papers), professor, and at the time of my retirement, Director of the Graduate Program in Neuroscience and Animal Behavior at Emory University. I will hold off making any comments about my overall impressions of this book until after we have had a chance to get together to discuss it. However, as I was reading the book I was frequently thinking to myself that some topics did not seem to be described in a manner that would allow a reader with little or no background knowledge to fully understand what was being discussed. Perhaps I am wrong about this judgment, but in any case I am going to attempt to write up a few short tutorials about topics mentioned in the book and post them here. Not sure how many of these I will get to or how fast I will complete them so I will attach them individually as separate comments (scroll below to ‘replies’) to this  post as they are completed. I welcome others with knowledge about these topics, or specific questions they would like to have addressed, to post their own comments to this post.

Ron Boothe

About Ron Boothe

I am a Professor Emeritus at Emory University, currently living in Tacoma Washington USA.
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5 Responses to Pre-discussion Tutorials for Topics Mentioned in From Bacteria to Bach and Back

  1. Ron Boothe says:

    On page 7, Dennet states, “For instance, mutation in DNA almost never occurs—not once in a billion copyings—but evolution depends on it.”

    This statement is accurate based on recent scientific studies that involve direct measurements of mutations in bacteria, but needs to be put in a broader context to understand its significance for the topics Dennett covers in this book. Keep in mind that the DNA strands that makes up the human genome are made up of over 3 billion base pairs. So, using the 1 in a billion number for mutations in a human would lead to the simple calculation that we should expect to pass on about 3 mutations to each of our children. Taking into account some technical differences between how DNA is replicated in bacteria and humans, current estimates for humans are somewhat higher; we can expect to pass on somewhere around 60 mutations to each of our offspring.

    That number, 60 mutations passed on to each of our offspring, also needs clarification to be meaningful. About 90% of the base pairs in our DNA do not appear to do much of anything (sometimes called ‘junk DNA’). So, 90% of the mutations probably occur in junk DNA and are not likely to have any effect on the offspring. Furthermore, most of the remaining mutations that occur in functional parts of the DNA are likely to have such bad detrimental effects on the offspring (miscarriages, stillborns, etc.) that they will not be carried into the next generation. What we really want to know in terms of what is relevant for evolution is how often a mutation survives into future generations of humans.

    We can gain some empirical evidence about how often that happens by comparing human DNA to that of our closest living relatives, chimpanzees. We can trace the DNA present in humans and that in chimpanzees to a common ancestor that lived about 6 million years ago. Thus, any differences between our DNA and chimpanzee DNA must be due to mutations that took place over the past 6 million years AND survived to become part of the current human and chimpanzee genomes. Those mutations account for only about 1% of our genomes. Stated another way, close to 99% of the DNA found in humans and chimpanzees is identical – has not mutated in 6 million years.

    And yet, that small percentage of mutations is sufficient to account for all the observed differences between our two species, including the physical differences in our bodies, but also functional differences such as language and other cognitive abilities that are unique to humans, the topics discussed extensively in Dennett’s book. A number of those mutations have been studied extensively in recent years, and several have been discovered to relate to brain development and function.

  2. Ron Boothe says:

    In a section titled “The Cartesian Wound” starting on page 13 Dennett introduces the concept of Cartesian Dualism that derives from ideas promoted by Descartes in the seventeenth-century. Descartes argued that there are two realms of entities that exist in the universe, physical and non-physical. Our bodies including our brains are part of the physical world whereas our minds are part of the non-physical.

    Descartes’ dualism theory had to deal with the issue of how the body and mind could communicate with one other if they exist in different realms. That issue has continued to engage philosophers and scientists up until the present day. In modern parlance, it is commonly referred to as the Mind-Body Problem, or sometimes more specifically as the Mind-Brain Problem.

    Descartes’ proposed solution was to assert that the pineal gland has special properties that allow it to communicate with the mind. His rationale was based on an anatomical observation that there only appears to be one pineal gland and it is located near the middle of the brain whereas the other structures in the brain come in pairs, one on the left side and one on the right.

    There are actually two parts to the Mind-Brain Problem depending on the direction of the influence: 1) How does the brain, a physical entity, have an influence over the mind? 2) How does the mind, a non-physical entity, have an influence over the brain?

    The first part of the problem has to do with perception. If asked how our physical brain can give rise to sensations in our mind, modern cognitive neuroscientists would consider Descartes’ proposal that the answer has to do with special properties of the pineal gland to be silly. However, when analyzed carefully to make the assumptions explicit, many modern cognitive neuroscience theories can be demonstrated to be similar. For example, neuroscience textbooks often make claims that neurons in the visual cortex are responsible for producing visual sensations, those in auditory cortex for sound sensations, etc. Modern versions of these kinds of ideas are sometimes referred to as bridge locus theories because a fundamental assumption (often implicit rather than explicit) is that there are specific loci in the brain that are responsible for causing specific sensations. And it is important to emphasize that a large body of empirical results are compatible with bridge locus theories, so if this class of theories are rejected, some other kind of theory will have to be formulated that can account for those empirical findings. Over the past several decades there have been various attempts to formulate theories that do not involve bridge loci. Dennett proposes his own version in this book. In a nutshell, he is going to argue that Cartesian Dualism does not exist, and thus, a bridge locus would be a bridge to nowhere.

    When we address the second part of the Mind-Brain problem, influences of the mind on the brain, we are dealing with issues of free will. The physical brain is expected to operate according to deterministic laws of physics. Unless one believes in magic/miracles, there does not seem to be anywhere along the causal chain of brain events that would allow for free will to intervene. Descartes solved this problem by allowing the non-physical mind that does not have to follow the laws of physics to intervene in brain activity via the pineal gland. An alternative solution adopted by many modern cognitive neuroscientists is to deny that free will really exists. Since Dennett is going to eliminate Cartesian Dualism, his theory is likewise going to have to deal in some manner with the issue of free will.

  3. Sidney Whaley says:

    I really appreciate your comments as I found the book very confusing.

  4. Ron Boothe says:

    On page 16 Dennett states “People are calmly prepared to be instructed about the chemical properties of calcium or the microbiological details of cancer, but they think they have a particular personal authority about the nature of their own conscious experiences that can trump any hypothesis they find unacceptable.”

    My first time through reading the book I did not pay much attention to this sentence. Now that I have finished the book once and am working through it a second time, I realize that this sentence contains the crux on which Dennett’s entire argument rests.

    Due to my background as a scientist carrying out research on the topic of perception, I have a lot of experience grappling with issues about who holds the ultimate authority regarding the nature of an individual’s own conscious (in perception research, perceptual) experiences. Doing my best to not express any judgments here about Dennett’s position regarding this topic, I am going to try to explain the significance of this issue by discussing its implications in a different context.

    The scientific study of perception is concerned with percepts, the mental results of an act of perceiving. However, a scientist cannot observe someone else’s percepts directly. Therefore, the basic data that are collected by scientists studying perception are reports (in the form of words, symbols, or actions) by subjects about their own percepts. To make this more concrete, consider a scientific study in which a subject is instructed to look at a light on a sequence of trials and after each observation asked to report “yes” or “no” to the question “Did you see the light?” The data collected in this scientific study will be a series of responses recorded in a lab notebook; “yes”, “yes”, “no”, etc.

    Suppose the scientist decides to play a trick on the subject, and on a particular trial does not present the light stimulus at all (this is called a “catch trial”). Next, suppose the subject responds, “yes” on this catch trial. What is the proper way to treat that response? Common sense would seem to inform us that something is wrong here; the subject has reported seeing a light when no light was present.

    A few obvious possibilities are that the subject was in some kind of hallucinatory or dream state, was delusional, or was lying about what he or she actually perceived. So, for the purpose of this discussion lets stipulate that the subjects being studied have no psychological conditions or backgrounds that would make these kinds of explanations likely.

    How should this response be treated when it comes time to analyze and interpret the results from the experiment. Volumes have been written on this topic, but here I am only going to consider one specific way this situation has been handled sometimes in the past. Following a response of “yes” on a catch trial, the experimenter immediately provides feedback to the observer in the form of an admonition along the lines, “You just made a mistake. You reported that you saw a light when no light was even present. Further mistakes are going to mess up my experiment! Please stop doing it.”

    Does the scientist really have the “authority” to tell the subject he or she made a ‘mistake’?

    Let’s try another example. A scientist is carrying out a similar experiment with a monkey. Since the monkey does not have language to understand instructions or provide responses, the following procedures are substituted (we will ignore animal rights issues for purposes of this discussion). The monkey undergoes extensive training until it learns to reliably press a button whenever a bright light (that we know the monkey can see based on previous studies) is flashed. Following this training the light intensity is lowered to a level that we are not sure the monkey can see (determining that is the purpose of our experiment), and carry out some actual data collection trials that will be entered in the lab notebook; “button pushed”, “button not pushed”, etc.

    During this data collection we decide to include a catch trial in which no light stimulus is presented. The monkey pushes the button on this catch trial. A colleague suggests that we should make a change to our protocol. Following any button press on a catch trial, the monkey should be given a shock to the toe. This will be done in order to make the monkey stop making these ‘mistakes’.

    Does the scientist have good grounds (authority) for instituting this protocol?

    Here is the short answer that most modern day cognitive neuroscientists engaged in scientific studies of perception would provide for these kinds of questions: It depends on the precise way the question being asked of the subject is formulated. If the question asked is of the form, “Was a physical light stimulus presented on the last trial?”, then the scientist has the authority to label a positive response to a catch trial as being a mistake. If the question is of the form, “What did you perceive on the last trial?”, only the subject who provides the response is considered to be the ultimate authority. Detailed protocols need to be followed in order specify which kind of question is being asked before one can decide who has the authority to decide which responses are mistakes.

    Similarly, a detailed examination of the specific questions being asked will be required before we can evaluate whether or not “a particular personal authority about the nature of their own conscious experiences can trump [Dennett’s theory]“.

  5. Ron Boothe says:

    At the beginning of Chapter 5 on page 76, the first section heading is “Animals Designed to Deal with Affordances”.

    Then on page 79 Dennett provides a few sentences to give a cursory description of “J.J. Gibson’s (1979) concept of affordances: ‘What the environment offers the animal for good or ill.’”

    In the following chapter, on page 119, Dennett explains that his own “concept of information is a descendant of J.J. Gibson’s concept of affordances introduced in Chapter 5.”

    Footnote 30 on this same page acknowledges that Gibson’s concept is controversial: “Notoriously, Gibson doesn’t just ignore the question of what internal machinery manages to do this pick-up; he often seems to deny that there are any difficult questions to answer here. The slogan of radical Gibsonians says it all: ‘It’s not what’s in your head; it’s what your head is in.’ I am not endorsing this view.”

    Thereafter, the term affordances is used at numerous places in the book without further elaboration about its meaning.

    I doubt very much that any reader who is not already familiar with Gibson’s radical theory of Direct Perception (and those will be few and far between) will be able to appreciate Dennett’s appropriation of the term affordances into his own theory. Gibson’s theory is complex, controversial, counter-intuitive, and involves many logical arguments that are analogous to Dennett’s own “strange inversions of reasoning”. And both Gibson and Dennett are attempting to accomplish something extremely radical. In Gibson’s case he is trying to formulate a theory of perception that leaves out the brain. Dennett is trying to formulate a theory of consciousness that leaves out the mind.

    I was forced to become conversant with J.J. Gibson’s theory for a practical reason. Following J.J. Gibson’s death, his widow, Eleanor Gibson, spent several semesters as a visiting professor at Emory where she supervised graduate students. I sat on evaluation committees of some of those students and found it to be a frustrating experience since my own theoretical orientation was quite different from that of (so called) ‘Gibsonians’. I decided I needed to become more familiar with J.J. Gibson’s theory in order to be able to be more fair when evaluating the ideas proposed by these students, so I took a one-semester sabbatical leave during which I did nothing except read and think about the writings published by J.J. Gibson.

    Gibson’s theory is impossible to adequately summarize in only a few words, but I will try here to provide a one paragraph sketch of the essence of his theory. Traditional theories of perception assume that the physical environment does not cause our percepts directly, but only indirectly by stimulating the brain. Then the brain processes the information provided by the environment and ‘constructs’ our percepts. Gibson argued that there is no need to have the information in the environment processed. The information in the environment that is relevant for survival, argued Gibson, is so rich that it can just be “picked up directly” by the perceiving organism. The term Gibson used to refer to this information in the environment that can be directly picked up was ‘affordances’. By picking up affordances, an organism automatically knows what the environment offers (or affords) that is relevant for survival.

    For what it is worth, here is my evaluation of Gibson’s theory. If you had asked me how likely I thought a theory of direct perception along the lines that Gibson proposed could be successful before I spent an entire semester immersed in reading and thinking about it, I would have probably given a rating of no higher than 2 on a scale from 0 to 10. At the end of that immersion I still concluded that the theory had fatal flaws, but my evaluation of how close Gibson came to achieving his goal was raised to at least 8 out of 10.

    I will hold off making any evaluations of Dennett’s attempts to construct a similarly radical theory until after we have met to discuss his book.

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