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Our future, our universe, and other weighty topics

Tuesday, July 31, 2018

Compelling Heresy of the MOND Astrophysicists

Don't get cocky!”
Advice of Han Solo to Luke Skywalker, Star Wars Episode IV: A New Hope  

Cosmologist Ethan Siegel seems to enjoy serving as a kind of ideological stickler. Call him Ethan the Enforcer. Siegel fervently wants you to conform to whatever speculative dogmas are popular among his fellow cosmologists, whether it be the theory of dark matter or Guth's theory of a short burst of cosmic inflation at the dawn of time. Showing great overconfidence (like many of his fellow scientists), Siegel often speaks as if the cases for such speculations are slam-dunks, even though there is no strong case for either of these speculations. The things typically claimed as evidence for dark matter are mainly just things suggesting “something else,” some unknown reality, rather than dark matter specifically.

Sometimes Siegel writes kind of “whip the heretics” posts such as his recent post “There's A Debate Raging Over Whether Dark Matter Is Real, But One Side Is Cheating.” Siegel's purpose in this post is to demand compliance and conformity in regard to the speculative dogma of dark matter. He attempts to verbally flog those who prefer alternative theories, such as the theory of MOND (Modified Newtonian Dynamics), accusing such people of “cheating.” But he does nothing to substantiate such a claim.

Rather than assuming there are vast amounts of invisible dark matter, MOND theorists simply speculate that the laws of gravity are more complicated than Newton or Einstein assumed. Speaking of MOND versus dark matter, Siegel tells us that “Among cosmologists, there is no debate, because there is no alternative to dark matter that reproduces the observed successes.” This statement is false, and also clumsily enough contradicts the title of Siegel's post. There is indeed such a debate, and some cosmologists (such as those supporting MOND theories) don't believe in the dark matter theory. Siegel's untruth here is standard fare for ideological enforcers, who often take the tactic of exaggerating the popularity of whatever orthodoxy they are defending, while trying to sweep heretics and dissenters under the rug.

Siegel gives us this narrative about dark matter:

What's most impressive is that the predictions of dark matter were first made in the 1970s and 1980s, and were observationally confirmed later. This is not a case of tweaking the model to fit the data; this is a case of the best kind of science you hope for: where you make predictions, make the observations, and what you see validates and confirms the predictions you had made.

Such claims are rather amusing. Of course, the “best kind of science you can hope for” is when you directly observe something that you postulated before observing it (such as when Dirac predicted antimatter before it was discovered). But nothing like that has happened in regard to dark matter, which has never been directly observed, and which has no place in the Standard Model of Physics. As for predictions, theorists have been constantly fiddling with dark matter theoretical models over the past few decades to try to get them to fit observations, and there is still a large degree of discrepancy between observations and such models, particularly in regard to satellite galaxies.

Andromeda galaxy and one of its satellite galaxies (credit: NASA)

In his zeal to flog his ideological opponents, Siegel fervently tells us, “It's only if you ignore all of modern cosmology that the modified gravity alternative looks viable.” For a cosmologist to accuse other cosmologists of ignoring all of modern cosmology is an example of heated rhetorical excess that will not persuade anyone that Siegel is coolly and calmly pondering this weighty topic.

Below is a table found on the “Mond Pages” website defending MOND cosmology. The table compares the dark matter theory (shown in red) to the rival MOND theory. According to the author, the MOND theory actually holds up to observations better than the dark matter theory. The MOND theory seems better at predicting smaller scale reality (such as the situation around our galaxy and its satellites). The dark matter theory works better only on the largest scales. In his post Siegel trumpets the better performance of dark matter theory on the largest scales, neglecting to tell his readers about all the many ways in which the MOND theory outperforms the dark matter theory, particular at smaller scales.


Siegel's claim of cheating is based on the flimsy complaint that the MOND theorists aren't being honest about how dark matter theory works better at the largest scale. But, to the contrary, in the diagram above a MOND theorist seems to candidly admit that this is where dark matter theory does better (in the rows at the end of this table). No sign of any cheating going on here.

In this interview, a MOND supporter lists many problems with the dark matter theory. He states the following (using the acronym LCDM to refer to the dark matter theory) :

The hard-core cosmologists are more convinced than ever that LCDM has to be right. It has obtained the status of a religion. Among astrophysicists who are paying attention but aren’t too deeply entwined with cosmology, there seems to be growing skepticism. But it depends on what they’re paying attention to. The closer you get to cosmology, the more it must be so. The further you get, the more absurd it sounds.

In this post, the same person states that the search for dark matter has become a "quagmire of confirmation bias." If so, it isn't the only such quagmire on the landscape of science academia. 

Friday, July 27, 2018

Peddling the Great DNA Myth, They Flip-Flop Inconsistently

For reasons I discussed in my previous post and also in this longer post, the evidence is overwhelming that a specification for the human body plan does not exist in DNA. But some scientists continue to push the myth that DNA is a specification of the human body plan. An example of a scientist doing such a thing is a recent book entitled How to Code a Human: Exploring the DNA Blueprints That Make Us Who We Are by biologist Kat Arney. Arney's wavering claims about DNA flip-flop all over the map, and we can frequently find one claim she makes on this matter that contradicts other claims she makes on this matter.

Let us look at the wildly inconsistent claims that Arney makes about DNA.

Claim #1: DNA simply has recipes for making molecules. This relatively modest claim is made on page 9 of Arney's book, where she says, “Genes are recipes for making molecules.” The same claim of genes as recipes is made on pages 34 to 35. Even this relatively modest claim is not correct, because DNA merely specifies an ingredient list for molecules such as protein molecules. DNA does not specify the three-dimensional shapes that such molecules need to have in order to be useful.

Claim #2: DNA consists of genes that are “living entities.” On page 8 of her book Arney says this:

Instead of being like computer code, with tidy electrical circuits, genes are more like recipes. They are living entities, full of constantly shifting molecules and with many options for flexibility, depending on the range of things a cell needs to manufacture.

In this statement, we have multiple glitches. First, computer code does not contain electrical circuits. Second, genes (particular sections of DNA) are chemical units (fractions of a molecule) that are not living entities. Third, you contradict yourself very obviously if you first say that a gene is a recipe (a lifeless, inert thing), and then in your next sentence claim that a gene is a living entity. Fourth, a gene is part of a DNA molecule, not something “full of constantly shifting molecules.”

Below is an example of a recipe, and it includes both an ingredient list and assembly instructions. Neither DNA nor the genes in it are recipes, for they do not contain any assembly instructions. Nowhere in DNA or one of its genes is there anything like an assembly instruction for making a cell, a tissue, an organ, an organ system, an appendage such as an arm, or a full organism. DNA is written in a bare-bones “amino acid language” that is so lacking in expressive capability that it is impossible that DNA could ever even have assembly instructions for a simple cell, a unit of such complexity that it is often compared to a small city.

Recipes include assembly instructions

Claim #3: DNA is like computer code, and “directs the processes of life.” The title of Arney's book about DNA is “How to Code a Human.” The title implies that DNA is like some computer software that specifies the functionality of how human biology works. Also on page 6 Arney tells us that “the genetic information encoded in our DNA directs the processes of life.” But such a claim is inaccurate. Since DNA has only one-dimensional information specifying chemical ingredients, it could not possibly be something that “directs the processes of life.” And claims about DNA being like computer code that “directs the processes of life” are inconsistent with Arney's claim on page 8 that “instead of being like computer code” genes are “more like recipes.” Recipes don't direct things.

Claim #4: DNA is some kind of agent that directs embryonic development. This claim is made on page 116 where Arney claims that genes “direct embryonic development” and that “genetic rules and patterns" guide embryonic development. These claims are contradicted by her confession on page 7 that “scientists are only just beginning to find the answers to some really big questions such as: how does a fertilized egg divide and specialize to make all the tissues of the body?” When a scientist says that his colleagues are “only just beginning to find the answers” to some matter, it essentially means they don't understand the matter and know almost nothing about it. So how then can Arney possibly be claiming that genes “direct embryonic development”?

Arney provides no evidence to back up her claim that genes “direct embryonic development,” other than mentioning the feeble evidence of Hox genes, the role of which is murky. Having failed to back up this claim, she resorts on page 125 to saying, “There is not enough space in this book to go into the details of human development and the genes that direct it.” We may be forgiven for concluding that the real reason she is not listing any solid evidence for the claim that genes direct embryonic development is that such evidence does not exist and cannot possibly exist (given the expressive limits of DNA), not that there was not enough space in her book.

Claim #5: DNA consists of blueprints. This claim is made in the subtitle of Arney's book, which is “Exploring the DNA Blueprints That Make Us Who We Are.” The claim the DNA consists of blueprints is inconsistent with Arney's previous claim that DNA consists of recipes. A blueprint is a specification of the three-dimensional layout of something, and according to the usual understanding of a blueprint, a blueprint does not include assembly instructions. In this sense it is the opposite of a recipe, which does include assembly instructions, but does not specify the exact physical layout of the final product. The claim that DNA consists of blueprints is also inconsistent with Arney's previous claims that genes “direct the processes of life” and “direct embryonic development.” Blueprints are passive things that don't direct anything. A blueprint is not an agent.

As for claim #4 and claim #5, they are both explicitly debunked by Agustin Fuentes, a professor of anthropology, who states the following:

Genes play an important role in our development and functioning, not as directors but as parts of a complex system. “Blueprints” is a poor way to describe genes. It is misleading to talk about genes as doing things by themselves.

In statements such as this, scientists "fess up" that the idea of DNA as a human specification is not true. Two other scientists "fess up" in a similar way when they write the following about genes in the journal Nature: "Population genetics is founded on a subset of coding sequences that can be related to phenotype in a statistical sense, but not based on causation or a viable causal mechanism."

Regarding the DNA as blueprint idea (claim #5), a wikipedia.org article entitled “Common misunderstanding of genetics” lists the claim that “Genes are a blueprint of an organism's form and behavior” as one of the “common misunderstandings of genetics.”

These five claims by Arney are wildly inconsistent, and all over the map. DNA cannot be an agent and a director if it merely consists of blueprints; and if it consists of blueprints, it cannot consist of recipes; and if genes are blueprints, they cannot be like computer code, which works totally different from a blueprint. When you hear someone throwing out such a variety of claims that conflict with each other, you should suspect that their claims lack a foundation in fact. And that is the case here.

In its article on “molecular genetics,” the Stanford Encyclopedia of Philosophy says the following:

The fundamental theory that says the role of DNA is to provide the information for development has been criticized on many grounds....Philosophers have generally criticized the theory that genes and DNA provide all the information and have challenged the use of sweeping metaphors such as “master plan” and “program” which suggest that genes and DNA contain all developmental information....It is not clear that they can elucidate the idea that genes are "fundamental" entities that "program" the development and functioning of organisms by "directing" the syntheses of proteins that in turn regulate all the important cellular processes. In fact, there is considerable skepticism in the philosophical community about this fundamental theory.

Another relevant article in the Stanford Encyclopedia of Philosophy is its article on developmental biology. That article tells us that there is no theory explaining how the development of an organism occurs. We read the following:

It is uncommon to find presentations of developmental biology that make reference to a theory of development. Instead, we find references to families of approaches (developmental genetics, experimental embryology, cell biology, and molecular biology) or catalogues of “key molecular components” (transcription factor families, inducing factor families, cytoskeleton or cell adhesion molecules, and extracellular matrix components). No standard theory or group of models provides theoretical scaffolding in the major textbooks (e.g., Slack 2013; Wolpert et al. 2010; Gilbert 2010). The absence of any reference to a theory of development or some set of core explanatory models is prima facie puzzling. Why is it so difficult to identify a constitutive theory for developmental biology?

These assertions contradict Arney's claim that genes “direct embryonic development.” Evidently such a theory has not become very widespread, for the quote above makes clear that there is simply no general theory of what causes embryonic development.

Arney contradicts herself all over the place when talking about DNA and genes. A similar lack of consistency on this topic is found in an Aeon essay by biologist Itai Yanai. Below is a quote:

At the most fundamental level, then, our genome is not a blueprint for making humans at all. Instead, it is a set of genes that seek to replicate themselves, making and using humans as their agents. Our genome does of course contain a human blueprint – but building us is just one of the things our genome does, just one of the strategies used by the genes to stay alive.

The biggest problem here is not the anthropomorphic nonsense about genes seeking things and “using humans as their agents,” but the glaring contradiction of saying in one sentence “our genome is not a blueprint for making humans at all,” and then saying two sentences later, ”Our genome does of course contain a human blueprint.” That's another case of a scientist saying something false, and adding an “of course” to compound the error. See this post for why genes and DNA cannot be truthfully considered a blueprint for a human being.

In this post entitled “DNA is a recipe, NOT a blueprint,” a PhD student in “molecular evolution” debunks the claim that DNA is a blueprint, asserting emphatically, “Describing the genome as a blueprint is a recipe for disaster.” But the author then asserts the equally incorrect idea that DNA is a recipe, saying it “is much more accurate” to describe DNA as “a recipe or set of instructions for making the organism.” No, it no more accurate to describe DNA as a recipe than to describe it as a blueprint, because there is in DNA no “set of instructions for making the organism,” no set of instructions for making an organ system, no set of instructions for making an organ, no set of instructions for making a tissue, no set of instructions of making a cell, and not even a lowly set of instructions for making a single three-dimensional protein molecule. DNA has merely the chemical ingredient lists of proteins.

Advancing the Great DNA Myth that DNA is a human specification, our biologists flip flop all over the map, contradicting each other, with a single biologist often contradicting himself or herself on this topic.

Jonathan Latham has a master's degree in Crop Genetics and a PhD in virology. In his essay “Genetics Is Giving Way to a New Science of Life,” a long essay well worth a read, Latham exposes many of the myths about DNA. He states the following:

A standard biology education casts DNA (DeoxyriboNucleic Acid) as the master molecule of life, coordinating and controlling most, if not all, living functions. This master molecule concept is popular. It is plausible. It is taught in every university and high school. But it is wrong. DNA is no master controller, nor is it even at the centre of biology....Does DNA have any claim to being in control? Or even just to be at the centre of biological organisation? The answer is that DNA is none of the things Watson, Lander, and Collins claim above, even the standard, supposedly nuanced, biologist’s view of life is wrong...The evidence that DNA is not a biological controller begins with the observation that biological organisms are complex systems. Outside of biology, when we consider any complex system, such as the climate, or computers, or the economy, we would not normally ask whether one component has primacy over all the others.....Geneticists, and sometimes other biologists, make this linear interpretation seem plausible, not with experiments—since their results contradict it—but by using highly active verbs in their references to DNA. DNA, according to them, “controls”, “governs”, and “regulates” cellular processes....However, there is no specific science that demonstrates that DNA plays the dominant role these words imply. Quite the opposite....It is habitually, but lazily, presumed that DNA specifies all the information necessary for the formation of a protein, but that is not true....How is it that, if organisms are the principal objects of biological study, and the standard explanation of their origin and operation is so scientifically weak that it has to award DNA imaginary superpowers of “expression” and “control” to paper over the cracks, have scientists nevertheless clung to it?

It seems that just as many of our theoretical physicists have taken to indulging in what may be called Fantasy Physics, such as string theory and multiverse speculations, many of our biologists have been indulging in Fantasy Biology. One of the main aspects of Fantasy Biology is the claim that DNA is a human specification, something it cannot be because of its own inherent expressive limitations, which must prevent it from specifying anything a hundredth as complex as a human specification. Another of the main aspects of Fantasy Biology is the claim that human memories are stored in synapses, a claim that cannot be correct because memories can last 50 years, but the average lifetime of a synapse protein is less than a month, which means writing to a synapse would be as unsuitable for permanent storage as finger-writing in the wet sand at the edge of a seashore. In both cases, Fantasy Biology commits the sin of ignoring a physical limitation that should have constrained our thinking on a topic. 

Monday, July 23, 2018

Why DNA Cannot Be a Specification of a Human

The discovery of DNA was one of the great triumphs of science. But ever since this discovery there has been a strange trend which we may call “DNA inflation” or “DNA exaggeration.” The trend has been to carelessly describe DNA in ever more grandiose terms, regardless of the actual facts.

One very common claim is that DNA is a blueprint that lays out the complete specification of the human body. Another common claim is that DNA is a recipe (or a library of recipes) for making an organism. It is also sometimes claimed that DNA is like a computer program for generating our bodies.

But such statements are not warranted by the facts. Judging from the facts, we must conclude that while DNA uses a code of symbolic representations (the genetic code), DNA is not a blueprint for making a human, is not a recipe for making a human, and is not a program or algorithm for making a human. The facts indicate that DNA is not anything close to a complete specification of an organism, but that DNA is instead something much simpler, mainly just a kind of database (or a collection of ingredient lists) used in making particular parts of an organism.

To get an idea of the true nature of DNA, it is a good idea to adopt a conceptual model of DNA. In science, a model is a somewhat simplified representation that helps us understand a more complicated reality. A classic example of a model is the Bohr model of the atom, in which the nucleus of an atom is compared to the sun, and the electrons in an atom are compared to planets that revolve around the sun. The atom is actually more complicated than such a situation (given the weirdness of quantum mechanics), but the Bohr model is still useful to help us get a basic grasp of what an atom is like. The Bohr model is essentially accurate, because just as the great majority of a solar system's mass exists at its center in the sun, the great majority of an atom's mass exists at its center in the atomic nucleus.

Now, what model can we use to grasp the basic nature of DNA? A good model to use is what we may call the chain-of-colored-beads model. Let us imagine a long chain of colored beads, in which there are about twenty possible bead colors, and each bead stands for a particular type of chemical called an amino acid. That is exactly how DNA works. We can imagine that one of these colors means kind of “Start.” The amino acids are the constituents of proteins. So after one of these “Start” beads appears in the chain, there is then a sequence of colored beads, with each color representing one of the twenty amino acids. Altogether the long “chain of beads” that is DNA specifies the ingredients of thousands of different proteins.

A particular snippet or section of DNA will correspond to a chain of amino acids that is the starting point of a protein. The visual below illustrates this schematically.

polypeptide chain

Now, once we have adopted this useful “chain of colored beads” model to help us understand the nature of DNA, we can understand the limitations of DNA. What type of information can be specified with such a “chain of colored beads”? Only simple linear information, what is called one-dimensional information. As two scientists state, "Genes are merely a means of specifying polypeptides," the one-dimensional chains like those depicted above. 

An example of one-dimensional information is a telephone number, a social security number, or a stock ticker tape. Such information can always be presented with a single line or row, although some types of one-dimensional information might require a long line or row. A more complicated type of information is what is called two-dimensional information. Such information requires both rows and columns. An example of two-dimensional information is the information in a calendar or a spreadsheet.

Another more complicated type of information is called three-dimensional information. Three-dimensional information specifies something that can only be described using the dimensions of length, width, and depth. An example is the information specifying the three-dimensional structure of a car.

Now, what type of information would be required to specify the physical layout of a three-dimensional body such as the human body? To specify such a thing, you would need three-dimensional information, information involving length, width and depth. But there is no way that such three-dimensional information could exist in DNA, which has merely one-dimensional information.

In fact, it seems that in order to make a complete biological specification of an organism, you would need not just three-dimensional information, but four-dimensional information. Time is often regarded as the fourth dimension. We can describe four-dimensional information as information that involves not merely aspects of length, width, and depth, but also an aspect of time.

Why would you need four-dimensional information to specify an organism such as a human? For one thing, it is not true that humans just pop into existence as adults. Instead, there is a long series of transitions between the earliest state of a newly fertilized egg, and that of a full-grown human. A full human specification would have to specify each of these states. So the specification would need to use the fourth dimension of time to specify this temporal progression in human forms.

Another reason why a full human specification would need to be four-dimensional is that human beings are not static objects, but intensely dynamic objects. Think of all the dynamic activity occurring every day in your body. Blood and electricity is flowing about, proteins are being synthesized according to specific time tables, cells are being born and dying according to other time tables, and so forth. A single snapshot of the state of a human body is not at all sufficient to capture this dynamic activity. You would need to have a specification that is four-dimensional. Similarly, if someone from some small island in the Pacific had no idea of what a city was, you would never specify what a city was by just showing some maps. You would need to somehow specify the motion occurring in the city: the subways moving, the cars moving, the people moving, the water flowing through pipes, and so forth.

But DNA can only specify one-dimensional information. So it is very absurd to maintain that a biological specification of humans is in the one-dimensional information of DNA.

The table below lists on the left various types of information that would be needed to have a full biological specification of an organism, and on the right whether or not such information can be specified in DNA.

Type of information Can it be specified in DNA?
Linear amino acid sequence of a protein molecule Yes
Three-dimensional shape of a protein molecule No
Exact location where a protein is located in body No
Layout of a cell organelle No
Layout of a cell No
Layout of a tissue type No
Layout of an organ No
Layout of an organ system No
Layout of a full body plan No
Structure progression from simplest tiniest form to fully grown form No
Dynamic behavior inside an organism during a particular month or year No

Some would disagree about the answer I have given in the third row, and claim that the three-dimensional shape of a protein molecule is purely a consequence of its sequence of amino acids. If this were true, scientists would have long ago solved the protein folding problem, and would be able to predict the three-dimensional shapes of proteins from their one-dimensional sequence of amino acids. But after decades of trying to do this, the protein-folding problem is still unsolved, and (as discussed here) scientists still cannot accurately predict the 3D shapes of large proteins from their amino acid sequences.

The fact that DNA can only store one-dimensional information is a decisive reason for rejecting all claims that DNA even half-specifies the human organism. There are two other reasons for rejecting such claims. The first is that no one has found any information in DNA corresponding to human body plan information. The human genome has been thoroughly studied through massive projects such as the Human Genome Project and the ENCODE project. No one has found any gene information specifying a human body plan, a structural plan for a cell, a structural plan for an organ, or a structural plan for an organ system.

The second reason is equally enormous. It is simply that there exists nothing in the human body that could interpret a specification of human biology, if such a thing existed in DNA. Consider computer code. Such code can only work because there is an enormously sophisticated piece of software called an interpreter or compiler that is smart enough to read such complex instructions. If it were to happen that DNA stored instructions for making a human, contrary to the evidence, we would only explain human development if we imagined that somewhere in our biology was some enormously sophisticated machinery or functionality capable of reading such highly complex instructions and executing them. But no such functionality has ever been discovered.

Is it accurate to say that there are recipes in DNA? No it is not. A recipe includes an ingredient list, and a set of instructions explaining how to make a particular meal or dish using those ingredients. DNA has lots of ingredient lists specifying the ingredients of proteins. But nowhere does DNA specify a series of instructions for assembling a protein molecule, a cell, an organ, an organ system, or a full body. Protein molecules have three-dimensional shapes that they assume for unknown reasons. Such shapes are not specified in DNA.

At the end of this post (in which I cite additional very weighty reasons for rejecting the claim the DNA is a specification of a human), I quote eight different scientists (mainly biologists) who state that DNA is not a recipe or blueprint for making a human, or anything like a specification of the human form.  

So where is it that biological shapes and structures come from? This is a gigantic unknown, which stands as a dramatic contradiction of all attempts to explain biology in mechanistic or materialistic terms. We do not know where the 3D shapes of protein molecules come from. We do not know where the shapes of cells come from. We do not know where the structure of tissues comes from. We do not know where the shapes of organs come from. We do not know where the shapes of organ systems come from. We do not know where the overall body plan of an organism comes from. We therefore have a strong reason to suspect that such things are mysterious inputs from some unfathomable reality outside of an organism.

The reality of DNA is something very inconsistent with the claims about DNA made by many a science book, where we hear about DNA as a blueprint for the body or DNA as some recipe for making a human. In my next post I will look at one of these books, and the false and wildly inconsistent claims the book makes about DNA. We will see that the tall tales that the book tells about DNA are five different claims that are all inconsistent with each other, resulting in a kind of DNA mythology that is “all over the map.” 

Postscript: The genome is an organism's DNA, while the phenotype is the set of observable characteristics of an organism (such as its external appearance and internal arrangement of organs). In the mainstream book "Frontiers in Ecology, Evolution and Complexity," a scientist states the following:

At the beginning of the 21st century, biology confronted an uncomfortable fact: despite the increasing availability of whole genome sequence data, it was not possible to predict, or even clarify, phenotypic observations. In fact, we now know that there is not sufficient information in the linear DNA of the complete genomes to recover and/or understand the diverse phenotypic states of an organism. 

In statements such as this, scientists "fess up" that the idea of DNA as a human specification is not true.  Another example can be found in this paper written by several scientists, in which we read this: "Because genes code for proteins, there are no 'genes for' phenotypes per se, including behavioral phenotypes."  Here is another example. "DNA cannot be seen as the 'blueprint' for life," says Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland.  He says, "It is at best an overlapping and potentially scrambled list of ingredients that is used differently by different cells at different times."  Sergio Pistoi (a science writer with a PhD in molecular biology) tells us, "DNA is not a blueprint," and tells us, "We do not inherit specific instructions on how to build a cell or an organ." Michael Levin (director of a large biology research lab) states that "genomes are not a blueprint for anatomy," and after referring to a "deep puzzle" of how biological forms arise, he gives this example: "Scientists really don’t know what determines the intricate shape and structure of the flatworm’s head."

Agustin Fuentes, a professor of anthropology, states the following:

"Genes play an important role in our development and functioning, not as directors but as parts of a complex system. 'Blueprints' is a poor way to describe genes. It is misleading to talk about genes as doing things by themselves."

Two other scientists "fess up" in a similar way when they write the following about genes in the journal Nature: "Population genetics is founded on a subset of coding sequences that can be related to phenotype in a statistical sense, but not based on causation or a viable causal mechanism."

Regarding the DNA as blueprint idea a wikipedia.org article entitled “Common misunderstanding of genetics” lists the claim that “Genes are a blueprint of an organism's form and behavior” as one of the “common misunderstandings of genetics.” Jonathan Latham has a master's degree in Crop Genetics and a PhD in virology. In his essay “Genetics Is Giving Way to a New Science of Life,” a long essay well worth a read, Latham exposes many of the myths about DNA being a blueprint or master controller, and points out DNA does not even fully specify a protein. He states, "It is habitually, but lazily, presumed that DNA specifies all the information necessary for the formation of a protein, but that is not true." 

Ian Stevenson M.D. cited quite a few biologists pointing out the genes and DNA cannot determine the form of an organism:

"Genes alone - which provide instructions for the production of amino acids and proteins -- cannot explain how the proteins produced by their instructions come to have the shape they develop and, ultimately, determine the form of the organisms where they are. Biologists who have drawn attention to this important gap in our knowledge of form have not been a grouping of mediocrities (Denton, 1986; Goldschmidt, 1952; B. C. Goodwin, 1985, 1988, 1989, 1994; Gottlieb, 1992; Grasse, 1973; E. S. Russell...Sheldrake, 1981; Tauber and Sarkar, 1992; Thompson, 1917/1942)."

Biologist B.C. Goodwin stated this in 1989: "Since genes make molecules, genetics...does not tell us how the molecules are organized into the dynamic, organized process
that is the living organism."

Thursday, July 19, 2018

The BRAIN Initiative's Floundering Quest for a Mechanistic Account of Mind

The BRAIN Initiative is a multi-year big-science project launched during the Obama administration in 2013. It started off in 2014 with a budget of about $110 million, and its funding has increased in subsequent years, with some estimating that it may use up billions in funding before it is finished. One of its documents claims on page 121 that the BRAIN Initiative ”will require new and distinct funding of between 300-500 million per year." Too bad the program consists largely of not-terribly-useful research designed to try to prove an extremely dubious mechanistic ideology about the mind.

The assumptions behind the project are made clear in a document called Brain 2025: A Scientific Vision, which is offered at one of the project's two main web sites. The “scientific vision” laid out in the document is largely an ideological vision, based on the far-fetched idea that the human mind is merely the product of the brain. The dubious ideology of the authors is made clear in the very first sentence of the document, in which the authors state, “The human brain is the source of our thoughts, emotions, perceptions, actions, and memories; it confers on us the abilities that make us human, while simultaneously making each of us unique.” It has certainly not been proven that any brain has ever generated a thought or stored a memory.

In fact, later in the document the authors confess, “We do not yet have a systematic theory of how information is encoded in the chemical and electrical activity of neurons, how it is fused to determine behavior on short time scales, and how it is used to adapt, refine, and learn behaviors on longer time scales.” This is certainly true. No one has anything like a systematic theory of how a brain could store memories as neural states, nor has anyone come up with anything like a systematic theory of how a brain could generate a thought. So why, then, does the document start out by stating that “the human brain is the source of our thoughts, emotions, perceptions, actions, and memories”? No one has any business making such a claim unless he first has “ a systematic theory of how information is encoded in the chemical and electrical activity of neurons,” but the document admits that no such theory exists.

The document makes clear that the main purpose of the BRAIN Initiative will be to shore up mechanistic ideas about the human mind. The document states, “The most important outcome of the BRAIN Initiative will be a comprehensive, mechanistic understanding of mental function that emerges from synergistic application of the new technologies and conceptual structures developed under the BRAIN Initiative.” That makes it pretty clear that the project is ideology-driven. The idea that mental function can be explained mechanistically is a very doubtful piece of ideology inconsistent with many forms of evidence. One of these forms of evidence involves the many cases of minds that worked well after half or more of the brain was lost to injury, disease or surgery. Another such form of evidence is that scientists cannot find any plausible storage place in the brain where memories could be stored for 50 years, synapses (subject to very rapid molecular turnover) being no such thing.

What are some of the things that this BRAIN Initiative will be spending money on? Most of the project's money will apparently be spent as follows:

  1. Trying to develop new tools to study the brain.
  2. Creating circuit maps of the brain.
  3. Identifying various types of brain cells.
  4. Playing around with zapping people's brains in various different ways.

There is no reason to believe that any of this activity will actually result in the project's goal of a “comprehensive, mechanistic understanding of mental function” or even something much smaller, a fragmentary mechanistic understanding of mental function. There is no “circuit map” that we can possibly imagine that would allow us to understand how neurons might produce thoughts, how neural activity could result in such a thing as selfhood, or how human episodic memories could ever be stored as neural states. No real insight into such things has been produced by previous efforts to identify different types of brain cells or map out the connections of the brain. So why should we believe that any further insight on these matters will come from further activity along these lines?

In a section entitled “Manipulating circuit activity,” the Brain 2025 document tries to suggest that electrically zapping people's brains might tell us something about memory. It says, “In the 1950s, Penfield’s electrical stimulation experiments suggested that a memory or thought could be elicited by activating neurons in the underlying network.” But the document fails to tell us that a review of 80 years of electrical stimulation of the brain found that it was very rare for people to recall anything during electrical stimulation of the brain and that Overall, only one patient reported what appeared to be a clearly detailed episodic memory for which he spontaneously specified that he had never thought about it.” But nonetheless the BRAIN Initiative fellows expressed great enthusiasm for monkeying with people's brains. After noting approvingly that “stimulating electrodes are being placed in human patients,” the BRAIN 2025 document says, “Entirely new tools could be developed based on magnetic stimulation, gases, infrared excitation, ultrasound, or organic or physical chemistry to allow access to neurons deep within the brain.” It sounds like their plan is kind of like this:

master plan

So far the BRAIN Initiative has been running for four or five years, and has accomplished nothing extremely noteworthy. Our understanding of the brain has not dramatically advanced during those four or five years, and all the old mysteries of mind and memory seem as mysterious as ever. At this “Achievements” link there is a discussion of what the BRAIN Initiative has accomplished so far. At the top of the text is a big bold headline saying “Transformative Advances,” but the BRAIN Initiative has produced no such transformative advances. Go beyond the flashy spin on the web site, the high-tech glitter, and the discussion of things in progress that haven't yet yielded much, and you have not a single major accomplishment relating to our understanding of the mind or memory. You see in this section a video entitled “The BRAIN Initiative – the First Five Years.” The video fails to list a single accomplishment of the BRAIN Initiative. Apparently all this work to mechanistically explain the mind is pretty much a flop and a failure so far.

About the only memorable thing mentioned in the BRAIN Initiative's list of accomplishments is a description of some “brain interface” by which a paralyzed person was able to use to raise a robot arm to bring a cup to his mouth. Such an interface doesn't seem very impressive when you consider that the same effect could have been achieved much less expensively and more simply by using a 1990's-style voice-based interface that would respond to a command such as “raise arm.”

I predict that even after spending billions, the BRAIN Initiative will by 2025 produce no big breakthrough in our understanding of mind, memory or consciousness. All attempts to understand such things through mechanistic methods (such as creating circuit diagrams or zapping brains) are doomed to failure. The reason is that mind, memory and consciousness are not mechanistic products of the brain, but are aspects of a human soul or spirit that cannot be understood by analyzing electricity, neurons and chemistry. If our minds were produced by brains and our memories were stored in brains, we would have already discovered by now “smoking guns” of such mechanistic effects; but no such things have been found.

We found in the 1950's that all cells have encoded information in the form of the genetic information in DNA. If our brain cells contained encoded memory information, we would have discovered abundant fingerprints of such a thing during the twentieth century. But even though it is 65 years after DNA was discovered, and even though our electron microscopes can see things 1000 times smaller than synapses, no one has discovered any proof of memories encoded in neurons. Such a mechanistic encoding would require thousands of dedicated genes, to accomplish the gigantic task of translating our experience and ideas into neuron states; but not one such gene has been found, even though the human genome has been thoroughly studied. There is one scientific study claiming to have found correlation evidence for such memory-encoding genes, but the study's methodology is quite goofy, for the reasons discussed at the end of this post. 

A better approach for gaining insight about the mind would be one that focused on extraordinary human experiences, and people having ordinary mind and memory function despite extraordinary brain states. This would involve studying all the people whose minds functioned well even after they lost vast parts of their brains due to surgery or disease, all the people with phenomenal memories despite having ordinary brains, and all the people having extraordinary experiences such as near-death experiences and out-of-body experiences, often while their brains were shut down. Such a study approach would tend to shed light on how mechanistic neuroscientists are making the wrong assumptions about the brain. 

Postscript: A long 2019 article in the Atlantic discusses the poor results of the Human Brain Project (HBP). The author states, "the people I contacted struggled to name a major contribution that the HBP has made in the past decade."

Sunday, July 15, 2018

The Exit Doors of Paradise: A Science Fiction Story

When David Deloren was abducted by extraterrestrials, he thought it would be the start of a terrifying experience. He never expected that he would have more fun than he had ever experienced.

David saw the glowing disk-shaped UFO while hiking in the wilderness. He came up directly underneath the UFO, to get a good look. Then he saw some beam coming from the UFO toward him. He was astonished to find himself being levitated into the air. He was lifted up into the UFO, and then saw some strange creature inject him with something. He quickly fell into unconsciousness.

David awoke to find himself on a comfortable bed. He was in a room that looked like an expensive hotel room. Exiting the room, he walked around before finding a room filled with other humans, most of whom seemed happy and cheerful.

Where am I?” asked David. “I think I was abducted by a UFO.”

Oh, another new abductee?” said a young woman with a big smile. “Well, don't worry about a thing. You'll be plenty happy here. Let me fetch Mr. Hawkins to give you a briefing.”

After a short delay, Mr. Hawkins came into the room to give David an introduction to his new surroundings.

Welcome, to what we call the Place of Pleasure,” said Mr. Hawkins. “In this wonderful location, all of your pleasure needs will be abundantly fulfilled.”

Where is this place?” said David. “Why was I brought here.”

I can't tell you that,” said Mr. Hawkins. “But I can tell you that you will be able to live here for as long as you wish. Nothing will be asked of you. Just enjoy yourself.”

David began to explore around, and soon found out about the abundant opportunities for pleasure at his strange location. The location resembled a big resort and amusement park. There were swimming pools all over the place, all filled with warm, clear water. The swimming pools all had long fun slides. There were many cafes and restaurants, all offering free food. The food was better than any he had ever tasted. In each cafe was a singer and musician who sang songs that seemed to David more beautiful than any he had heard before.

David soon learned that his strange location was some kind of sexual paradise. Every day he would be approached multiple times by amorous young ladies eager for sensual enjoyment. Most of them had faces like movie stars or supermodels. Before long he learned that 80 percent of the local people were robots. But in the bedroom, he could not distinguish between the robots and the real humans. The real humans were all abductees like himself. All of the abductees had been treated with injections that removed any danger of disease or unwanted pregnancies. There was also something in the drinking water that greatly intensified all sexual experiences.

David also learned that at this strange location, he could drink alcohol to his heart's content, without ever getting drunk or without his mood being negatively affected. The only effect was that the alcohol made him merrier and more likely to laugh. David also found he could use recreational drugs to his heart's content, enjoying the highs of cocaine and heroin, without any of the danger or drawbacks he would have experienced using such drugs on Earth. The drugs were offered for free in the cafes, and listed on the menu signs. When David once asked whether there were any legal penalties for using the drugs, the people in the cafe simply laughed very hard. He assumed from then on that in this place no one went to jail for using drugs.

David was in a wonderland of pleasure, enclosed by a huge high dome with the color of a blue sky. He sometimes asked himself: could it be that this whole location was part of some extraterrestrial spaceship?

There was only one way out of the location. There were two tall doors that were clearly marked as an exit. A strange hooded figure always stood near those doors.

One day David walked towards the figure and asked about the exit doors. He could hardly see the face underneath the hood, but it looked non-human.

Can I see what's outside the doors?” asked David.

Yes,” said the hooded figure. “But if you use these doors, your exit will be permanent, and you can never come back to this place of perfect pleasure.”

What lies beyond these doors?” asked David.

Knowledge,” said the figure. “Vast and deep knowledge. If you go beyond these doors, you will learn all about why you were brought here, all about the extraterrestrials who abducted you, and all about many other deep truths of time, space and cosmic history.”

So what's it like past those doors?” asked David.

Maybe life is hard past those doors, or maybe it is easy,” said the hooded figure. “I can't say. But it won't be half as much fun as this place of perfect pleasure you are leaving behind.”

Then to hell with it,” said David. He went back to his bodily pleasures. But after ten more days of sex better than any he had known on Earth, and food better than any he had known on Earth, and more blissful drink and drug experiences, he began to keep thinking again and again about the exit doors. He kept thinking about what kind of deep cosmic knowledge he might find by going out the doors.

After another week passed, David returned to the exit doors, and found the same strange hooded figure in front of them.

You said there was great knowledge to be found by going past those doors?” asked David.

Yes, vast and deep knowledge, knowledge of great cosmic truths,” said the hooded figure. “But if you pass through those doors, you must leave behind forever this place of perfect pleasure. And I give no guarantee about how easy or hard it will be when you pass through those doors.”

Let me through,” said David. “My body wants to stay here forever, but my mind and soul want me to go through those doors.”

Very well,” said the figure. “You will learn many great truths.” He unlocked the doors, and opened them.

For starters, how about telling me why I was brought here,” said David.

This whole place is merely an experiment,” said the figure. “It was built for only one purpose – to find out what percentage of you humans will ask to pass through these doors. If that fraction is high enough, then my primeval race will have found out the human race is worthy of entering into fellowship with we who have roamed the galaxy for a hundred million years.”

Wednesday, July 11, 2018

The Flaws in His "Origin of Language" Experiment

In 2017 Evolutionary biologist Kevin N. Laland produced a book entitled “Darwin's Unfinished Symphony: How Culture Made the Human Mind.” The book had an odd subtitle. How could culture have made the human mind, when a mind like the human mind was needed for culture to have even got started?

Chapter 8 of the book is entitled, “Why We Alone Have Language.” Laland presents a theory of the origin of language, but it's not a very useful one. His theory addresses the “why” of the origin of human language, not the “how” of the origin of human language. Anyone can come up with reasons why humans might have found it useful to originate a language. The hard part in regard to the origin of language is explaining the “how” part. This involves addressing questions such as these:

  • How could a language ever have got started, when it seems that you need to have a language in place in order to teach anyone a language, or to impose a language on a group of people, so that they all speak the same language?
  • How could a language ever have got started, considering that language requires lots of specialized speech biology in the mouth and brain, which wouldn't have existed when someone first tried to establish a language?
  • How could anyone have contrived any original rules of grammar, the origin of which is so much harder to explain than someone merely thinking up some nouns and words, and convincing nearby people to use those words and nouns?

Laland's theory of the origin of language is that language was created to teach people things. Laland specifically suggests that language was created so that people who knew how to make stone tools could pass on that knowledge. To try to back up this idea, Laland has done some experiments. He had 200 adult experimenters work in experiments described in his book as follows:

Adult human participants first learned to knap stone flakes using a granite hammerstone and flint core, and then were tested on their ability; next, they helped others learn this skill....Experimental subjects were allocated to one of five conditions that varied according to the type of information that could be passed from “tutor” to “pupil.”

The five conditions included an “imitation” condition in which pupils could only imitate another person they were watching, a “gestural teaching” condition in which a teacher could only silently make gestures to try and teach how to make stone tools, and a “verbal teaching” condition in which teachers could speak instructions to their pupils. The experiments showed that teaching someone how to make stone tools occurs more effectively when you can use language such as modern English – but only slightly so. A scientific paper describing the experiment says in Table 1 that the “total quality” of the teaching of how to make stone tools was 23.6 with verbal teaching and 19.8 with gestural teaching.

Laland sounds very pleased with his experimental results, and at the end of the chapter, he makes it sound like they offer some evidence of great importance. He says this:

Alfred Russel Wallace, codiscoverer of natural selection, famously failed to accept that selection could account for human evolution, partly because he could not imagine how a trait like language, and the other unique features of human cognition, could evolve. I would like to believe that, had he known of the material in this chapter, he might have reached a different conclusion.

But Laland has failed to see two fatal flaws in his experiment. I can explain the first flaw by mentioning that humans can only speak clearly because of a great deal of specialized biology, biology which humans would presumably not have had when the first humans tried to speak. This biology is mentioned on page 174 of the book How Language Began by Daniel L. Everett, who states the following:

The creation of speech requires precise control of more than one hundred muscles of the larynx, the respiratory muscles, the diaphragm, and the muscles between the ribs – our “intercostal muscles”-- and muscles of our mouth and face – our orofactal muscles. The muscle movement required of all these parts during speech is mind-bogglingly complex.

And here Everett is not even mentioning specialized biology in the brain. Stroke victims often lose much of their ability to speak. So there is not only a good deal of the brain specialized to allow speech, but also a good deal of speech-specialized biology in the area around the mouth, throat and lungs. There is no natural reason why humans would have had so much speech-specialized biology when humans first started to speak.

The flaws in Laland's experiment are as follows:

  1. He has compared the effectiveness of gesture-teaching of stone making skills to the effectiveness of speech-teaching of stone making skills, using modern humans who have mouths and brains optimized for speech. When language originated, according to naturalistic assumptions, humans would not have had such biology.
  2. He has compared the effectiveness of gesture-teaching of stone making skills to the effectiveness of speech-teaching of stone making skills, using modern humans who could use the full grammatical amd vocabulary richness of modern speech. When language originated, according to naturalistic assumptions, no such linguistic richness would have existed.
  3. His experiment only allowed a five-minute teaching period, which did not allow any “hand gesture” teachers a decent amount of time to teach some hand signals to be used in the instruction.

I can imagine how you could modify Laland's experiment to get a more realistic result. The first change in the experiment would be for all the "speaking allowed" teachers to have had mouths filled with food when they tried to teach how to make stone tools. This would simulate the fact that the first people trying to use spoken language would not have had any mouths optimized for speaking, and would only have been able to speak garbled words, making the kind of hard-to-understand sounds a person might make if his mouth was filled with food.

A second modification in the experiment to make it more realistic would be to forbid the teachers from using any language other than a language they invented themselves. So, for example, a teacher might be allowed to invent the word “crob” to mean “rock,” and then to teach that word to someone; and a teacher would be allowed to invent the word “soz” to mean “strike,” and then teach that word to someone. But a teacher would not be allowed to use instructions such as the English sentence, “Now firmly grip the big stone with your left hand and strike it at a 45 degree angle with the smaller stone, using your right hand.” The third change would be to allow all subjects to have up to an hour to teach, allowing someone a decent length of time to teach some hand signals or newly invented words that could later be employed as part of the instruction.

With these three modifications, the experiment would realistically simulate whether  it would be more effective for teachers at the beginning of a language's origin to teach using hand gestures or using rudimentary speech. The experimental results would be drastically different. Instead of finding that the teachers trying to use speech were slightly more effective than the teachers using gestures, it would be found that the teachers using gestures were able to teach much more effectively.

Why is that? It's because it's much easier to convey information using nice, clear hand signals than by using spoken language whenever spoken language sounds all garbled and unclear, as it would have sounded if humans first started to use spoken language before getting all the specialized biology in the mouth and brain allowing spoken language to be clearly transmitted.

There is a paradox I call the IPS paradox. IPS is an acronym standing for Inferiority of Primitive Speech. I can describe the paradox or difficulty as follows:

  1. Before any spoken language, it would have been possible for humans to communicate fairly effectively and clearly using hand gestures, in which particular words are expressed by particular hand gestures.
  2. If humans first started speaking before developing all the specialized biology needed for clear speaking, they would only have been able to speak in a very unclear and garbled manner, like a modern person trying to speak while holding his tongue against the bottom of his mouth, or trying to speak with a mouth filled with food.
  3. Such a primitive mode of oral communication would have been greatly inferior to hand gestures as a mode of communication.
  4. It therefore seems that oral language never could have become established before organisms developed good speech biology like modern humans have, and that there would never have been any gradual progression from primitive, garbled speaking to the type of clear speaking like humans now have.

I argued for this Inferiority of Primitive Speech paradox in a previous post. Laland's experiment does nothing to remove that paradox. His experiment allowed people with modern anatomy to use regular English sentences to teach stone-making. That does nothing to clear away the difficulty that it would have been a hundred times harder to orally teach something at the dawn of language, at a time when human ancestors did not have all the nice biology current humans have allowing them to speak clearly, and when no language was yet established. The Inferiority of Primitive Speech paradox is a powerful reason for rejecting all theories of the naturalistic origin of human spoken language. We can understand how humans might have naturally developed a hand gesture language, but cannot understand how humans could have naturally developed the first spoken language with rich expressive capability and complex rules of grammar.