Our understanding of the laws of the genetic code?

[Suppaman]

I just did my morning exercise while listening to a short youtube talk on genetics. I do not understand it but what struck me was it seemed to be on the level of an EE discussing OHM's law, Transistor theory, and digital logic terms.

Now I know all the rules that make my PC on which I am writing this question existed thousands of years ago and were waiting to be discovered and used. I do not believe we have reached a point where we can explain how the basic rules for the genetic code can make us, you and me and my cat now telling me it is her breakfast three time.

I think the laws for genetic code and what can be made from that code existed millions and millions of years ago. Having a building in some cave somewhere producing my PCs without human intervention seems unlikely. However, we seem to have been lucky that the original design specification of the things made by the genetic code does just that. My question is, how well do we understand how this genetic code can make a human baby (or a cow or a fish or in the good old days a T-Rex?)

Thank you for indulging my curiosity.

 

[jim mcnamara]

I am giving you a very non-technical answer, just as you seem to want.

We understand the basic "system" very well. Once a strand of DNA is assembled, researchers can tell you a lot about it example:
what protein it can provide the blueprint for. Sometimes many different proteins may result from one protein, because these proteins can be worker drones to make other things, like a final product tooth enamel.

The problem is very simple to understand but requires lots of research to give you all of the possible answers. There are very complicated ways that the DNA can be switched "on" to make proteins, and switched "off" to not make proteins. Example:

Hormones. Imagine you are hiking, and out of the bushes comes a giant grizzly bear. It scares the bejeebers out of you. You immediately start running, your heart rate, respiration rate increases, and lots of other changes happen including mental state changes. All of this is from one tiny molecule that a few cells in your body manufactured, called adrenaline (the 'fight or flight' hormone). Many changes happen with your DNA as a result of getting scared. Some DNA gets turned off and some turned on.

All from one tiny molecule. Humans have the ability to make about 50+ hormones that control all kinds of things from hunger to sleepiness.

So into this mess you have your DNA strand. So what will it do? What mix of hormones are out there running around? Also note, we left out the large variety of other possible controlling factors that might be out there. So it gets even worse than you might think - in order to answer 'what does my small chunk of DNA do?'

Learning what DNA does for living beasties may be very, very hard. Researchers have worked for a long time to begin to get some good understandings.

Short answer: DNA worked the same for T-Rex as it now works for humans, rose bushes, and goldfish.

Quick, simple video:

 

[Suppaman]

Thank you for your comments and the video was very understandable. It seems we have a lot going on that allows us to live and procreate.

My background is in quality assurance. When I test something, I need a specification. I am not talking philosophy here, just practical nuts and bolts. As we learn more about how this genetic tool works we can document the rules and even the tolerances that apply. Eventually, we should be able to know what everything does. Also how to modify, to improve, to expand the specification.

If you look at everything a human (or any living) being works it is marvelous. My question is, are the physical laws of the universe the ones that caused this specification to exist? The specification we document as we learn more. If they do, that would explain how life evolved.

As each of life's development stage is entered these rules would guide the end results. This universal law would also strongly suggest life is common in the universe. And because it is likely, we are not an elder race we may find much more advanced beings.

I worked for over 12 years on the development of a time of flight mass spectrometer. It only worked when things were done that physics said were possible. I believe that we can do improvements in life if we have a specification and can do simulations. Sometimes I feel I was born a thousand years too soon.

Thank you for your reply. Links to places that are documenting this human design specification are welcome.

 

[Ygggdrasil]

When people speak of the genetic code, they are referring to the code for translating a DNA sequence into protein. This code has been known for over half a century, and at this point it is very well understood. However, this genetic code does not tell us everything we need to know about biology and there are a few different levels of knowledge that are missing. While proteins are important functional units inside the cell (e.g. they carry out chemical reactions, act as structural units to organize the cell, and help to control which genes are turned on and off), knowing a protein's sequence is not always sufficient to tell us the protein's function. We are making progress in this area, however.

One problem here is the protein folding problem. Given the sequence of amino acids that make up the protein, can we predict the three dimensional shape that it folds into. Knowing the shape of the protein is important for understanding it's function (and is very useful if you want to design drugs to target that protein). There are a variety of programs and algorithms that scientists have designed predict protein structure. These programs make use of existing knowledge, first comparing the protein sequence to a database of protein sequences of known structure to build an initial model, then uses physics based models to refine the structure prediction based on how different amino acids within the protein are known to interact. Predicting protein function works in similar ways; a program will compare a protein of unknown function to a database of proteins with known functions to make an educated guess. However, these predictions are not perfect, and much more work is needed to be done.

To get an idea of the scale of the problem, consider a study where scientists pared down a bacteria's DNA down to the smallest number of genes required for the bacteria to survive. Of the 473 essential genes, about 30% of them were of unknown function. This is a major challenge if we want to start building computer simulations of life.

Protein functional predictions is also a very important topic in medicine as DNA sequencing technologies become more common in clinical settings. When doctors sequence a patient's genome, they will find that the patient's DNA contains many different mutations. Sometimes, it's very clear that these mutations may be disease causing (e.g. if they disrupt an important part of the protein or are mutations that have been catalogued previously as having a pathogenic effect), sometimes it's clear that the mutations are likely to be benign (e.g. a silent mutation that does not result in a change to the protein's sequence), but in many cases, the mutations get classified as https://www.ashg.org/education/csertoolkit/uncertainresults.html (VUSs). Better tools to understand how protein sequence dictates protein structure and function would help doctors better diagnose VUSs.

There is a much larger problem, however. Of the roughly 3 billion base pairs that comprise the human genome, only about 2% of those code for protein. It is estimated that ~ 10-20% of the human genome contains important non-coding DNA that does not code for protein, but plays other important roles, such as regulating gene expression. For many of these non-coding regions, we don't really have a good understanding of how DNA sequence encodes function.

 

[DaveC426913]

My question is, are the physical laws of the universe the ones that caused this specification to exist?

That is what our best theories tell us, yes.

If they do, that would explain how life evolved.

Do you mean how life has evolved?
Or do you mean how life evolved from non-life?

Different questions.

 

[Suppaman]

Marvelous! We think we know some of the puzzles, there is a lot we know that we don't know. And once we know all of this, we will probably not yet understand what provides this ability. Thank you for taking the time to write. I remember asking someone what was the "probability" for these folding rules to be developed randomly and they answered longer than the universe would probably exist.I remember reading about a bird that needed the blackest feathers, and it had improved their blackness by using some material properties that were very sophisticated and resulted in a very optically black black. I wondered at the time how this was done by evolution. I do not think evolution is random; it has some feedback loop governed by, what, the laws of physics?

How the bird's mate who preferred the best black was able to tell black from very black and how evolution discovered the optical engineering ability to make the birds color most black. It occurred to me this ability, for some unknown reason, was part of the genetic code just waiting to be discovered by evolution.

If my job were to discover how all of this worked, I would know that I would be very constrained on what real life testing would be permitted. Computer simulation is very near, combine a quantum computer and an AI, and we have even bigger questions. As soon as we know what we can do and shortly how to do it the human will become part of the loop of evolution. Perhaps that is part of the rules?

Thank you all, I have my answer, at least I believe I do. That is acceptable.

 

[Suppaman]

That is what our best theories tell us, yes.Do you mean how life has evolved?
Or do you mean how life evolved from non-life?

Different questions.

I think life originated because some attribute of the physical laws of the universe are such that life must evolve. As best as I know, no one knows how they were established but it is likely creating life was a useful byproduct. Works for me. Thank you for asking.

 

[jim mcnamara]

IF you want details about how life got started - as far as our current knowledge: Abiogensis 101 in a video

 

[Suppaman]

Very interesting and seems to validate that life is not luck but environment. Thankyou.

 

[Drakkith]

I remember asking someone what was the "probability" for these folding rules to be developed randomly and they answered longer than the universe would probably exist.

I'd say that these folding rules are far from purely random. Given some amino acid sequence, there are only a limited number of ways for the sequence to fold into a stable protein. Evolution has selected for those amino acid sequences which can consistently fold into useful shapes and are stable under normal cellular conditions. Sequences that don't meet this criteria are selected against.

I do not think evolution is random; it has some feedback loop governed by, what, the laws of physics?

Evolution is caused by both random and non-random processes. Natural selection, for example, is very non-random. Given some change in the trait of organisms in a population, that change will tend to spread over time if it is beneficial, and will tend to be suppressed and/or disappear if the change is harmful. Neutral changes are subject more to genetic drift, which is a random process.

Of course, the mutations that lead to these changes are themselves entirely random.

How the bird's mate who preferred the best black was able to tell black from very black and how evolution discovered the optical engineering ability to make the birds color most black. It occurred to me this ability, for some unknown reason, was part of the genetic code just waiting to be discovered by evolution.

One of the issues here is that you're describing both changes in behavior and changes in physical traits. Physical traits are by far the easier of the two to understand, as many traits can be mapped down to a handful of genes or less. Changes in behavior are much, much more difficult to understand. Changes in behavior are caused by changes in an organisms nervous system, be that a change in the physical structure (the way neurons are connected together) or a chemical change (change in amount of a neurotransmitter, or the structure of a specific protein used by neurons for example).

Understanding how even a simple organism's nervous system functions is extremely difficult. Fruit flies have thousands if not millions of neurons, far fewer than even the simplest vertebrate, and we only recently were able to make a full map of their brain. Without knowing exactly how an organism's brain is wired there is little chance to identify how specific mutations lead to behavioral changes.

 

[Rive]

We think we know some of the puzzles, there is a lot we know that we don't know.

A very disturbing problem about 'genetic code' is that 'nature' is not really interested in rules. What works, works: and seemingly every little critter strives to develop something unique based on the common foundations. So while we have some understanding about the foundations, it will require a lot of work till we can understand all the tricks of different species.

 

[pinball1970]

I think life originated because some attribute of the physical laws of the universe are such that life must evolve. As best as I know, no one knows how they were established but it is likely creating life was a useful byproduct. Works for me. Thank you for asking.

Its probably a good idea to have in mind what you mean by “life,” in the context you are considering.

If you have a dig around google you will come across candidates for the first self-replicating molecule, first membranes, proto cells and LUCA.

Also viruses, plasmids, viroids, I am not sure if you describe any of these as alive as such.