Biology

Why the Genome Incompletely Describes the Body

Genetic determinism—or the idea that we are fully determined by our genes taken from our parents—is now a thing of the past. Empirical evidence now shows that genes may exist but may not be expressed. The expression is controlled by some ‘epigenetic’ factors (which are also molecules) but enabled and disabled by the environment. OK, says the geneticist, let’s add the epigenetic stuff into the overall picture, and we can maintain the overall (materialistic) idea that living beings are molecular soups. However, the issue isn’t as straightforward, because there are potentially many things in the genes and the environment which can potentially create different outcomes. How do we select which genetic factors will interact with which environmental factors to decide a particular outcome? We need some theoretical insights that can demystify the issue of why genetic determinism fails.

What is the Genome?

It is widely accepted today that the genome carries information about the entire body. Even though the genome may not determine everything, it does determine many things—e.g. gender, eye color, skin tone, and so forth. However, the DNA material is only a fraction of what exists in each cell, which means that if the DNA is a picture of the body, it is a highly summarized picture. You can imagine taking a photograph of a large object—e.g. a mountain or an entire city—from a distance. If you are too close to the object, you will not get the entire object in view. But if you are too far from it, you will naturally miss a lot of details. Supposing that the DNA captures the picture of the entire body, it must miss out details, like a picture of a city that will not capture the tint of the glasses on somebody’s window.

The extent to which the DNA is missing information can vary. For instance, if you have a high megapixel camera, you can capture more details by making the size of the picture file larger. In terms of DNA, this would mean the presence of more genes. Conversely, a low megapixel camera will produce a smaller picture file, and correspondingly miss more details. The level of detail in the picture can be high if the span of the picture is smaller, or the detail can be reduced by increasing the picture’s span. This would correspond to the cases where the DNA captures some aspects very clearly, but the others are less defined. Alternately, all aspects can be captured, although each of them is weakly defined.

The fundamental problem is that the size of the picture is not an indicator of overall organism complexity. This is because you can have many types of pictures:

  • A large picture that ignores many details of an even larger object
  • A large picture that zooms into some aspects and neglects others
  • A small picture that ignores many details of a small object
  • A small picture that zooms into some aspects and neglects others

Since the picture can have a perspective, things ‘nearer’ to the camera would be detailed, and those farther would be hazier. That means, for the same size picture, you may get genetic determinism for some traits of the organism, but very little predictive ability about the other traits. It follows that we don’t just have to know the sizes of the picture and the object being photographed, but we also need to know the perspective from which the picture is taken. Without these, you can’t assume determinism.

The idea that we have a picture of the entire organism misses out two important things—the distance and the angle at which the picture has been taken. We are inclined to suppose that a larger object must have a larger picture, and everything must be photographed from a ‘nowhere’ perspective; in other words, all the details must be captured equally well. These presuppositions may not necessarily be true. So, the first intuitive way to understand the limitations of DNA is to just think of it as a picture of the body (as we currently do) but add to that picture an observer’s perspective—e.g. distance and direction—which can modify the representation of the body in a summarized form. There is some relation between the picture and reality, but the map is clearly not the territory. Accordingly, there must be greater determinism in some areas and lesser determinism in other areas.

The Properties of the Medium

The mirrors on the side of a car say: “objects are nearer than they appear to be” because the mirror is curved. While taking pictures, our cameras may produce the exact vision that our eyes see, but it is not necessary to think of the picture as even being observationally accurate if the medium in which we represent the picture—e.g. the mirror—is itself distorting the picture being represented.

This is again related to the observer’s perspective, but in this case, we are not talking about the distance and direction to the object being represented but about the properties of the camera itself. For example, the curved mirror can correspond to the lenses of the eye being distorted to create a conical, spherical, elliptic, or other types of representations which are all capturing reality, but in different ways. We cannot take the representation and know the reality unless we know the medium as well.

In ordinary mathematics, this corresponds to the idea that a number can be represented in different number systems—e.g. binary, decimal, hexadecimal, etc. So, the fact that you see two digits like ‘10’ may mean that this is 3 in the binary system, 10 in the decimal system, 16 in the hexadecimal system, etc. To store information, we need the convention in which it is stored. We assume that the convention of encoding remains unchanged, but that is not necessarily true. For example, the number system being used to encode numbers in the digits ‘10’ is meta-information not apparent from the digits. You cannot measure the digits and say that you know the exact value of the number. You must rather acquire this meta-information even prior to performing a measurement. In the same way, just observing the sequence of A, G, T, C, and U in the DNA doesn’t tell us what this means without the meta-information. If the meta-information is changed, then the same sequence can represent different information.

Compressing and Decompressing the Picture

If DNA is the summarized picture of the body, then we must expand this picture into the body. Since the summarized picture is not as detailed as the entire body, the missing information must be interpolated and extrapolated from the information present. We can imagine the process of trying to make a hazy picture that has a smaller pixel density into a sharper picture that has a greater pixel density. How do we add pixels to the picture to make it sharper, more detailed, and create new information?

One simple approach is called interpolation. The simple idea is that if a pixel (that doesn’t yet exist) is amid 4 pixels, then the pixel in between these pixels must be the average of the surrounding pixels. This ‘average’ can be computed by taking the mean of the hue, saturation, and intensity of the surrounding pixels. While useful in many scenarios, this method of averaging will not always work.

For example, imagine that I show you a zoomed in picture of a person, but you don’t know whether the portion of the picture being displayed pertains to the ear, nose, lips, or eyes. To interpolate and fill in the details, we must first know which part of the picture (e.g. ear, nose, lips or eyes) you are seeing. This means that we cannot interpolate locally (as in the above example of averaging). We must rather look at larger portions of the picture to even get the interpolation right. Effectively, the interpolation is not just with the immediately surrounding pixels, but with practically the entirety of the picture.

In terms of the DNA, you can say that I cannot expand a single gene to generate the specific trait of the body. I must rather consider the influence of immediately neighboring genes, which are likely to have a larger influence, but even this influence would be tempered by the other genes surrounding those neighboring genes and so forth until we have covered all the genes in the DNA.

Effectively, the idea that we have a linear sequence of genes that individually encode for a trait goes out the window because in trying to interpolate and expand the picture density I need to see the influence and relation of one gene on another gene. Clearly, some genes will be highly relevant to the effects created by a gene, while other genes will be less relevant. This ‘relevance’ of gene X in deciding the effect of gene Y cannot be known simply by measuring the presence of genes X and Y. We must rather consider all the genes in the DNA to understand any individual gene behavior.

A typical example of such interpretive nuisance arises in all texts, where, for example, something may be said on the first page of the book, and never said again, but it creates a context in which the last page of the book must be interpreted. So, the meaning of the symbols on the last page is not completely determined by the words (on the last page) but potentially by every other thing said in the book. For the genetic code this means that the exact effect of a gene can be changed by the presence or absence of numerous other genes. To determine the outcome, we must know the effects of genes on each other. The effect of one gene on another gene cannot be decided simply by presence and absence of genes. A more complicated method of determining their effect on each other is also required.

The Role of Quantum Theoretic Effects

Several additional problems arise when we try to think about the genes in terms of quantum theory. The first problem is that matter exists as a possibility rather than a reality. This basically means that even though all the molecules exist, they don’t necessarily create effects all the time. We normally think of molecules in a classical physical sense, which means that if something exists it must always produce an effect. But a quantum theoretic way to think about the problem is that the DNA is a possibility.

In concrete terms, we can say that the genes may exist but can lie dormant for long periods of time. As a result, we can say that somebody has a disposition toward disease (because the gene marker exists) but that doesn’t mean the disease is actively present. Gene markers for many diseases have been detected but they only indicate a probability toward acquiring a disease, not necessarily its onset. When and how a possibility becomes a reality remains a big unsolved problem in modern physics. Owing to that problem, when a gene becomes ‘active’ and when it lies ‘dormant’ is also unresolved.

The second problem due to quantum theory is that when a possibility becomes active, we don’t necessarily know which other possibilities it will interact with. In classical physics, a material object will either act with those molecules in its immediate vicinity (akin to the ‘collision’ of particles) or act everywhere and all the time (akin to the gravitational ‘force’ exerted by the particle). However, quantum theory quantizes this force; this means that there is a force particle (called a boson) emitted or absorbed to create an effect, but the time of emission and the destination it affects can’t be predicted. Therefore, not only can we not predict the time of an event, we cannot also predict its effect (as in the particle that is changed by the emission of this boson). Hence, the gene when it becomes active (after a period of dormancy) can create several different effects which cannot be predicted.

These two problems are consequences of treating matter as a possibility which entails that the cause becomes active occasionally and when it becomes active it can potentially create one of several possible effects (at different locations). Both the time of cause becoming active and the location of the effect created due to this cause remain unpredictable due to the unique nature of quantum theory. Unless this problem is solved in quantum theory, we cannot suppose that genes act always and have predictable effects. Making such an assumption would be tantamount to bypassing atomic theory.

The Fallacy of Evolutionary Theory

There are two interesting solutions to the problems of quantum theory which are relevant to biology.

The first solution corresponds to what we call the ‘environment’ in evolutionary theory. This solution is called Decoherence and it says that when two sets of possibilities interact with each other, some of mutual exclusive possibilities are eliminated. For example, if you spend time reading books and watching movies, while your friend spends time watching movies or playing sports, then when the two of you are present together, the alternative of reading books and playing sports is eliminated. Together the two of you can only spend time watching movies, because the other alternatives are mutually incompatible. The elimination of some possibilities creates a reality, and this idea can be understood as the effect of the environment on the organism. We can say that the environment ‘selects’ some possibility in the organism and suppresses others, which can be called natural selection.

The second solution corresponds to what we call random mutation in evolutionary theory. The problem is that this mutation is not random. Taken in the context of atomic theory, there is some agency—John von Neumann called this ‘choice’—which reduces the possibility to a reality. The mechanism of this choice, however, has been a subject of considerable debate and misunderstanding.

In summary, matter is a possibility, and this possibility is ‘reduced’ by two things—(a) the environment which selects some possibility and suppresses others, and (b) the choice which further selects from among the reduced possibilities. For example, if you were capable of spending time reading books, watching movies, or going out shopping, while your friend is only capable of watching movies or going out shopping or playing sports, then, you can eliminate some possibilities (e.g. reading books and playing sports) in an interaction, but you still have to make a choice between watching a movie or going out shopping. The main issue is that system interaction doesn’t eliminate all possibilities, although in many cases—e.g. in an adverse environment—it might limit the possibility to one.

The reality is that if you may have a strong inclination to discuss intellectual topics, you will not interact with another person who has no interest in that subject. You will rather seek someone in the environment with whom you can find areas of mutual interest. Therefore, what we call the ‘environment’ in evolution is not the only selecting agency; rather the organism can select the environment. That process of selecting the environment cannot be random and cannot be dictated by the environment. It must be determined by a choice, which evolutionary theory disallows.

As a result, what we call ‘random mutation’ in evolutionary theory corresponds to a choice in atomic theory by which we can select something to interact with—e.g. talk to select people, eat select types of food, living in select habitats, and so on. This choice or selection of the environment has had no material explanation so far in science, which means even though it exists, its effects are ignored.

The same problem appears in the case of genes when we consider epigenetic factors. The epigenetic factors are the ‘environment’ of the gene, and they select what becomes active in the gene. However, the gene can ‘mutate’ and thereby activate the epigenetic factors influencing it. There are two underlying mechanisms of selection—(a) that reject possibilities, and (b) that select possibilities. We can speak about the rejection of possibilities (as natural selection) but not about the selection of the environment due to random mutation, because the process is said to be random.

How Can We Understand Random Mutations?

The problem of choice in atomic theory and the problem of random mutations in evolution are connected, and they involve a new kind of causality, which can be understood if we think about individual desires which are used to make choices. Suppose you want to eat a certain type of food. Many kinds of raw materials may exist in your kitchen—your environment—but you pick some raw material to cook what you want. In other words, not everything in the kitchen is used, even though it exists. Our desire to eat something selects from the environment and then interacts with it.

But how do we get desires? A desire is the absence of something. But this absence is not always experienced. The absence rather manifests sometimes and disappears at other times. Whether the absence is manifest or unmanifest, it is always absent. So, we cannot ‘measure’ the absence like we measure presence. To understand how choice acts, we must postulate the causal effects of something that doesn’t exist, but it is experienced as the absence which forces a decision.

Inevitably, this brings in questions of past and future influencing the present into science. Everyone has commonsense notions about these effects, but scientific theories disallow these alternatives. The reason is that for something to be a cause in science, it must be measurable here and now. If you can’t measure something here and now, then it cannot be a cause. Since the past and the future cannot be measured here and now, therefore, they cannot be considered causes. However, when the world is a possibility, and causal interactions occur among these possibilities, then this limitation can be taken out. Something that exists in the future and the past exists right now but as a possibility—i.e. unobservable.

However, we need to distinguish the possibilities of now and those of the past and the future. Therefore, desire is a harder concept because it extends the problematic idea of possibility to past and future. If we can understand how matter exists as a possibility right now, then we can extend this existence to the possibilities in the future and the past, and then conceive their effect on the present. The problems created by quantum theory—where the world is to be described as a possibility—rains one revision to science after another. These things are not inconceivable, but just hard in modern thinking.

Imaginary Numbers in Physical Theories

A standard artifact of modern physical theories is the use of complex numbers, with real and imaginary parts. The real part is measurable, but the imaginary part is not. As I have discussed earlier, the imaginary component denotes additional ‘dimensions’ different from the real dimensions.

One way to understand these dimensions is to consider a higher space in which the lower space is an object. We can construct a hierarchy of spaces in which each space is an object for the higher space and a space for the lower object. The real part of the complex number represents the study of the world as objects, but the imaginary part depicts the same object as a space. This dual nature of the same thing signifies the relation between whole and part; the whole is the space and the part is the object. However, since the object is also a space, we need two descriptions—one to say that something is an object (the real part) and the other to say that it is a space (the imaginary part).

The problem is that we never measure this imaginary part in the real world. The reason is that when we observe the world, the external world is the object and our senses are the space. However, the senses are objects in a higher space called the mind, which is an object in a higher space called intellect, etc. So even though a ‘deeper’ reality is conceived mathematically, it is discarded while studying the external world because the external world is just objects and not the space that contains them.

They key outcome of the mathematics of atomic theory is that there is a hierarchical relation between things, but by describing the world as a world of things, we neglect this hierarchy. The hierarchy represents the priority of influence. For example, a higher object will influence the lower objects, but the lower object will only modify the influence of the higher object. This hierarchy can be used to solve the non-linear problems of mutual influence with thousands of interacting parts, but if the hierarchy is collapsed then which part influences which other parts (and when) becomes intractable.

The implication for genetics is that the genes in a DNA must also be viewed hierarchically. This means that some genes are very important, and the other ones are less important. Geneticists now believe that only 5% of the genes are expressed, which is an outcome of the fact that the effects of the other 95% are insignificant as they only modify the effects of the 5% genes. How we know the pattern of influence between genes and which ones are significant can only be understood by this hierarchy.

Summarizing the Challenges

We considered many kinds of challenges in understanding the genome thus far. To summarize:

  • The genome is a picture, but we don’t consider the perspective from which this picture is taken; as a result, we cannot say if something is more abstract or more detailed
  • The genome is encoded in a language, but we don’t consider the fact that the language could be different in each context, signifying different meanings from the same symbols
  • When the genome expands into the body, there is necessarily interpolation and extrapolation of missing information which comes from interrelations between genes, but we have no way of knowing which genes are being used for interpolation and extrapolation
  • Quantum theory tells us that genes are a possibility, not always activated. Even when they are activated, which aspects of the organism they will affect cannot be predicted
  • We have the bias of evolutionary theory in which the environment selects the traits in the organism, but the organism is not able to select the environment, or this selection is ‘random’
  • There are deeper reasons for this randomness which originate in the rejection of a direction or teleology in nature by which an organism can move in some chosen direction
  • We necessarily equate this teleology with a supernatural soul, when there are alternative models of causality involving the past and the future which could be used, but, owing to the bias in empiricism that the cause must always be measurable, these causes are rejected
  • There is a systematic mathematical system which employs complex numbers to describe the world, but the imaginary component of this description is discarded thereby creating the problem that the hierarchical relationship between the parts is neglected
  • Since this hierarchy determines which genes are more or less important, and the pattern of their interaction, neglecting this hierarchy means we cannot use genes to predict

All these factors contribute significantly to the misunderstanding of genetic determinism. The material complexity in nature requires a new causal model with possibilities, hierarchy, the activation of possibility by time, the selection of interacting possibilities, and the existence of causes that exist in the past and the future but influence the present. There is much more determinism than we can acknowledge within current science. The failure of current causal models presents avenues for new forms of causality.

The Role of Spiritual Choice in Biology

Now, someone can ask: What good is all this study if the main goal is to understand the ‘choice’ of the soul? The short answer is that the ‘choice’ of the soul is different from material ‘desire’. What everyone normally considers ‘free will’ is a material phenomenon. Matter automatically generates desires in us, but these desires involve a different kind of causality than employed in current science.

Many people would like to argue (somewhat prematurely) that because genetic determinism fails, there must be choice influencing the development of the organism. I would instead argue that before we can understand a transcendent choice, we must understand material desire and its effects. There is a subtle but important philosophical difference between ‘desire’ and ‘choice’; desires arise automatically due to matter, and the soul’s choices can reject these desires. Thus, what we call ‘free will’ at present is a material production, and the real spiritual production is ‘free won’t’ or the rejection of these material desires.

To understand the true nature of spiritual choice we need to segregate it from material desire. The standing conundrum of the mind-body problem in modern thinking can be resolved within matter. But a deeper level duality of soul-mind interaction requires a transcendent understanding.

The soul’s choices don’t control matter. Choice controls desire, and desire controls matter. So, if we can understand desire, then we have progressed toward understanding choice. The conceptual hurdle is that to understand desires in matter, we must measure absence and theorize why this absence becomes causally active (when we have a desire) but is unmanifest otherwise. To bring desire into the ambit of scientific conversation, many scientific revisions are needed. These will pave the way to a better understanding of why the soul’s choice is different from the material desire (and hence the soul is different from matter), but it can be used to control the desire.

We can also say that matter itself has goals or teleological behavior—because it produces desires. The soul is not the only source of teleology in matter. In current science we reject all teleology. We can progress to attributing teleology to matter, and then we can progress to the teleology created by the soul. The path to the understanding of the soul is treacherous because when we recognize that matter itself has goals—because it automatically creates desires—there would be a temptation to say that there is no soul because matter is itself goal-oriented. At that point, we must distinguish between the desire which appears as ‘free will’ and the choice which appears as ‘free won’t’ or the rejection of material desires. The soul and matter are different because matter creates teleology by producing this-worldly goals while the soul creates teleology by rejecting those goals.