Is DNA essence of life?


(Nonlin Org) #1

For a long time, and way before the discovery of its structure, DNA has been considered “essence of life”, the molecule that defines every organism including humans and that links ancestors with descendants over generations. Associations between DNA and heredity as well as between DNA and various hereditary traits have only enforced this view. Genetic code similarity between humans and other organisms seems to substantiate the tree of life and the story of evolution since we’re 99% chimps, 69% rats and 50% bananas according to the DNA. Recent computer developments lead us to the analogy between the DNA code and programming.

Is DNA essence of life? Are our development, appearance, behavior, and diseases pre-programmed in our DNA? Many connections have certainly been observed, but DNA is far from organism determinism. The information carried by the 3 billion base pairs of DNA nucleotides – each containing 2 bits of information (ACGT) – in the human genome amounts to only 6 G-bit of data which is less than 1 G-Byte (fits easily on a thumb drive). This is hardly enough to capture the complete manufacturing specifications for the simplest products around us like a pencil or a tire. Moderately complex systems like cars and airplane require a lot more data than available in a genome, and even that information is for high level recipes rather than complete (from atoms and simple molecules) instruction manuals.

A bit is a bit is a bit whether magnetic, silicone or DNA nucleotide. Some bits may certainly carry more important information than others, but only to the extent they link (index) to other information. “Fetch the human” can be encoded in a single bit if the only alternative is “fetch the chimp”. “Assemble or Fix a human” as in “transplant into a dying patient a cadaver hart” on the other hand requires a lot more information if this is to be carried out by a transplant surgeon in training – in fact this is the kind of information that may require on the order of Gigabytes in teaching materials. “Make a human” as “…from one zygote and the available atoms and molecules” is the type of request that demands an unknown number of bits, for certainly exceeding by many times the 1 GB of data available in the zygote’s DNA.

Does anyone believe that the differences between humans and chimps can be fully described in 8 MB of data? Scientific presentations that don’t even begin to scratch the surface of this topic take more than that computer storage space. Furthermore, 0.5% of our genome separates us from other humans while 1.2% separate us from bonobos and chimps. The implication is that our differences are more than skin-deep and cannot be explained by our similar genotype. The co-evolution story of chimps and humans that, given our similar genome, seemed plausible for a while, becomes much harder to accept if the genome is far less important than thought.

If not in DNA, then where exactly is the actual human blueprint? We do not have any strong leads, but we do know that even genetic twins are somewhat different, that epigenetics play a role, that some information is encoded chemically (as in redox reactions and DNA PCR), and that environment and the maternal womb are critical. None of these is a sufficient explanation however. Chemistry is common to all organisms, the environment can vary drastically without affecting the outcome that much (homeostasis), and the maternal womb is itself an outcome of a previous development.

What are the implications of ‘DNA not essence of life’? Most important (as discussed) is that “human just another ape” needs to be reevaluated, and that we need to seriously begin searching for this ‘essence of life’ somewhere else. Of smaller importance, revival of extinct species might be much harder than currently expected as would be chimera hybridization, and abiogenesis attempts currently focused on DNA and RNA might be futile.


(Matthew Pevarnik) #2

This video might help you:


(Chris Falter) #3

Speaking as a software developer, I can tell you that your reasoning, though sincere, is completely wrong. You can create amazingly complex software with well under 1 GB of instructions.

Moreover, 8 MB of difference in the instruction sets of 2 different programs can yield enormous differences of behavior.

I do affirm that there is more to being human than the instructions embedded in our DNA. The possession of free will must stand outside of our biological support systems, for example.

Grace and peace,
Chris Falter


#4

As a former software developer I can tell you that a single byte change in the right place can yield enormous differences. And yet any number of changes in other places yield no difference. As they say location, location, location. I would not be surprised if the same could be said for DNA.


#5

Heck, that could crash a jet fighter!


(Albert Leo) #6

Discussions on this subject can so often get derailed when nomenclature is not precisely understood by each participant. I think that the statement “DNA IS the essence of Life” is reasonable IF you are referring to all the kinds of life on earth. However, DNA, while necessary, is NOT sufficient, to define human life. Wallace was more prescient than Darwin in this regard. Describing a human as a “naked ape” is meant to be attention-getting–not a statement of either fact or scientific theory. In the effort to draw attention of non-scientists to the similarity between Homo sapiens and the primates who share our remote ancestry, we easily can (and have) sown confusion.

Biochemists are just learning just how unbelievably complex is a bacterial cell. Some of these microscopic bits of matter can carry out chemical reactions that baffle the most sophisticated chemists in today’s labs. So it may be foolish to search for Life’s Essence–an élan vitale. Unless, like me, you ascribe it to God. Perhaps the most difficult concept to fathom is how our Creator seems to want to covenant with one of his creatures. "What is Man that Thou art mindful of him?"
Al Leo


#7

In my experience, the one thing that seems to separate DNA from computer code is that DNA is more analog. The regulation of genes isn’t defined as a 1 or 0 like it is in binary code. Rather, upregulation or downregulation of a gene is more of a spectrum, like a dial on a stereo. Proteins and functional RNA molecules also follow this pattern, taking on different 3D structures depending on temperature, pH, salt concentrations, phosphorylation, glycosylation, and interactions with other protein/RNA molecules.

Looking beyond life we can find tons of examples where simple rules and simple chemical and physical interactions can produce very complex results, such as ice crystals, gem formations, solar systems, galaxies, and the like. We often refer to these types of relationships as emergent properties, akin to the old saw “the whole is more than the sum of the parts”.

I could be getting this completely wrong, but I remember one presentation where the presenter talked about nature operating from the bottom to the top while humans tend to design from the top down. Nature starts with simple rules and simple states, and through those interactions you get complex interactions and complex results. Humans tend to start with complex designs and complex interactions in order to get simple results. I have always found that to be an interesting comparison.


(Nonlin Org) #8

Chris, it pays to check your math before calling something wrong.
Here are some hints:

  1. ask your software engineering colleagues for their opinion
  2. compare against some very popular operating systems: Windows, Android, iOS, and keep in mind those still need the hardware to run
  3. read the initial post again. This passage might be illuminating: “the human genome … is less than 1 G-Byte (fits easily on a thumb drive). This is hardly enough to capture the complete manufacturing specifications for the simplest products around us like a pencil or a tire…”
  4. Keep in mind this is not indexing but full SW and HW specification. For simple Chimp/Human indexing of course you need exactly 1 bit.

(Nonlin Org) #9

Would you agree that a single byte (or even bit) can yield enormous differences only when indexing? Such as Chimp = 0, Human = 1? But that’s not what DNA does (most of the times), considering that it take three nucleotides to select one amino acid and up to tens of thousands of nucleotides to make one single protein. Indexing seems to happen in cases such as Down syndrome, and that only supports the assertion that DNA is not ‘essence of life’.

That’s not the case. Check again. There’s nothing analog in biology because it all comes down to discrete molecules and atoms. This is why Darwinian gradualism fails so badly as Mendelian genetics shows: http://nonlin.org/gradualism/


#11

I have no idea what you mean by indexing. A single bit change could change many things depending on where you change the bit. Indexing would not be involved, at least as far as what I understand indexing to mean.

Another difference between computer code and DNA is computer code always generates the same outputs no mater what environment it is run in. DNA on the other hand does not always generate the same proteins when the environment is different. Again, AFAIK.


(Roberto L Hernandez) #12

How is biochemistry digital and not analog?


(Chris Falter) #13

Exactly. According to previous posts by our friend Nonlin, everything is discrete and nothing is analog or continuous. Those old LPs? Not analog. AM radio? Not analog. Newton’s equations, which are expressed in terms of continuous variables over R? They don’t take discretization into account, so they must be wrong too. According to Nonlin.


(Nonlin Org) #14

This is not making any sense. Do you know the difference between discrete and continuum?

I gave you an example. If the bit references other information it’s an index. That bit references much more information that it can ever contain (see Shannon). This is the only way that a bit can “change many things”. Telling someone to produce you a human vs. a chimp is indexing. The information to produce that human from atoms and molecules cannot be possibly contained in 1 bit or even 1GB of data.

Are you kidding? Computers do sense and generate different outputs depending on the environment.

See here: http://nonlin.org/gradualism/. This was already posted.

We had this discussion before. This is about biology, not random subjects. At that time you agreed that biochemical reactions are indeed discrete. Review that discussion again. It’s quite simple, really. Meanwhile, did you figured out where your error was on ‘DNA not essence of life’?


(Chris Falter) #15

Hi Nonlin -

Your insinuations about my supposed need to re-read previous comments has no place in a forum like this.

I have never in any post agreed that discretization is the right way to model biology. I have always been painstakingly clear about that. That you seem to imply otherwise is quite baffling to me and probably to anyone who has read our conversations.

A continuous model can be a wonderful way to model a process whose discretization would make computation NP-complete (i.e., impossible). Yes, the continuous model’s result is an approximation, but if the approximation is good enough, it’s good enough.

Every branch of science employs this practice. To give one example from physics: the time it would take for a cannon ball to hit the ground is actually discrete, in the sense that the duration of the cannonball flight could (at least in theory) be described in a whole number of planck units. But does any physicist care about that level of discretization? Of course not! That tried and true continuous model, Newtonian physics, does the job quite capably. The model of Newtonian physics contains a small amount of error, but who cares? Newtonian physics provides the simplicity needed to make the cannonball trajectory prediction tractable. Insisting on making an accurate prediction in Planck units, on the other hand, would render billions of person-years of science and engineering a waste. Your insistence on needless discretization is no more helpful than proposing that we stop everything to count the whole number of angels that can dance on a pinhead. (No approximation allowed!)

Likewise in biology. The population genetics equations that underlie much of the theory of evolution are continuous, for example, but that fact is completely irrelevant to the question of whether they are good science. The only relevant question is whether they provide predictions whose accuracy is good enough. And they very much do.

Grace and peace,
Chris Falter

EDIT: Removed the idea of measuring the flight duration of a cannonball in planck units because I haven’t done the Heisenberg Uncertainty Principle calculations. I don’t remember how off the top of my head, and I don’t have the time to do the research.


(Chris Falter) #16

DNA gives a complete specification for the biological aspect of a human, given the environment in which that human lives.

However, I do agree with you that there is something about us that DNA cannot specify. Philosophers call that something free will. Theologians call it the image of God.

Grace and peace,
Chris Falter


#17

So 1 bit can only “index” to two possible values correct? But 16 bits together could point to 65,536 items correct? Now how many items could 1,000 bits point to? Try 1.2 quintillion or 1 followed by 30 zeros. I tried to do 1 GB but my calculator blows up so using your logic there should be no problem with the DNA indexing into as many different types of life as you care to imagine.

In terms of one bit changing many things, if you change one bit in a computer instruction you could change it from say add to subtract or from branch if true to branch if false. These will make a hugh difference in how the computer program runs and the outputs it generates.

The environment for a computer program is the data that it is sent. A computer program always generates the same results when given the same data.


#18

I don’t understand how that makes DNA any less analog (which I am using as more of an analogy). Chemical reactions produce a spectrum of products, contrary to the neat and tidy formulas that you drew up in chemistry. For example, when you react hydrogen and oxygen you get more than just water, you also get traces of hydrogen peroxide, free radicals, and other products. When a transcription factor is transcribed or translated it has a certain binding efficiency to different DNA sequence motifs which will produce a spectrum of binding states.[quote=“NonlinOrg, post:9, topic:36834”]
This is why Darwinian gradualism fails so badly as Mendelian genetics shows: http://nonlin.org/gradualism/
[/quote]

Given your inability to even understand what natural selection is, I think I will take your opinions on the theory of evolution with a rather large grain of salt.


(Nonlin Org) #19

Gradualism was Darwin’s assumption backed by no (none, nada, zero, zilch, zip) equations whatsoever, much less genetics.

This is not the topic here, but if you insist, I updated my "Discrete vs. Gradualism post to clarify to people like you:

Some argue that large collections of discrete points appear continuous, thus justifying gradualism. This view were acceptable if and only if the contribution of the discrete points were strictly cumulative (such as when many water molecules form water waves).

The list of discrete elements in biology includes but is not limited to: atoms, molecules, biochemical reactions, DNA, RNA, proteins, enzymes, genes, chromosomes, organelles, cell types (pro/eukaryote), cell division (mitosis/meiosis), sex type (male/female), body organs, organ systems, and organism classification. Changes at the discrete micro level including mutations and exposure to free radicals, radiation, and misfolded proteins are not cumulative and can potentially impact the entire organism. Continuous measure such as temperature, volume and weight are not true biologic properties (they apply to rocks and everything else) as these change over the life of organisms and are primarily statistical measures at population level in particular populations, environments and time.

Now, where is your list of proven continuous properties of organisms? Your computer models should represent reality, not pure fantasy.

Not possible, and you should know it, if indeed you learned anything at all about programming. This is not about free will, but about simple math and logic. No matter how badly you want to be right, 1 GB will not specify the simplest bacteria, let alone a human.

Look, you want to be right, but don’t seem to grasp the problem. Here is a clarification if data and computers are not your thing:
A bit is a bit is a bit whether magnetic, silicone or DNA nucleotide. Some bits may certainly carry more important information than others, but only to the extent they link (index) to other information. “Fetch the human” can be encoded in a single bit if the only alternative is “fetch the chimp”. “Assemble or Fix a human” as in “transplant into a dying patient a cadaver hart” on the other hand requires a lot more information if this is to be carried out by a transplant surgeon in training – in fact this is the kind of information that may require on the order of Gigabytes in teaching materials. “Make a human” as “…from one zygote and the available atoms and molecules” is the type of request that demands an unknown number of bits, for certainly exceeding by many times the 1 GB of data available in the zygote’s DNA.

Indexing is like searching on Google. You enter a few bits, but Google must have a massive database to answer correctly. Without that massive database, your search returns nothing.

And genes are expressed or not when given the same data (environment). No different.

The list of byproducts is still discrete. You’re not going to get any carbon molecules unless your reaction was impure and you can tally up the atoms and molecule to perfect precision.

Transcription factors are additional information representing development cycle, inter-cellular signals, the environment, cell cycle control, or pathogens. It’s obviously a complex system but all this is discrete information. Complex ≠ analog.

There’s no such thing as “natural selection”. It’s all hocus-pocus but that’s another topic.

What about “DNA not essence of life”? Do you understand the argument?


#20

They have been very much my thing for 40+ years and you don’t know what you are talking about.

You could say the old magnetic core memories stored a single bit in a single core, but at the level of silicon bits are stored in a variety of ways, charge in a capacitor, state of cross-coupled transistors, etc. You could say the base pairs in DNA are “bits” but the problem is the shape of the DNA strand also influences it’s action. Don’t know how you would encode that as ones and zeros but it is information just the same.

You are imposing you scheme for encoding information in DNA and I can assure you that you don’t have it right.

The information to train a surgeon is not encoded into DNA so I don’t know what you are trying to say here.

I haven’t brought up data compression yet, but if the data in DNA is considered to be compressed then it is possible that the 1 GB of data could be expanded into the equivalent of a much large data set. You could also view DNA as a program that can generate a large number of different outputs from a small program. I have seen small, as in less than 1000 bytes, programs that can generate an almost unlimited number of outputs.

Very different. Gene expression can change when the physical environment changes, such as the local ph. Look it up.


#21

“You keep using that word, I do not think it means what you think it means,”–Inigo Montoya

Gradualism doesn’t require a perfect continuum of morphological change, so I don’t know what you are on about. Gradualism simply means that a whole species transforms into a new species in a gradual and usually slow manner. This is contrasted by Punctuated Equilibrium where the population splits into many new species in a punctuated event. It is simply a contrast of the relative rates of change, and both do just fine with discrete units.[quote=“NonlinOrg, post:19, topic:36834”]
The list of byproducts is still discrete. You’re not going to get any carbon molecules unless your reaction was impure and you can tally up the atoms and molecule to perfect precision.
[/quote]

Again, I was contrasting biology to computer code which uses binary states. Biology and DNA does not use two discrete states in how it functions. Biology is much closer to analog, even if there are many discrete units when you focus down further. Again, I was just contrasting the two.

As an example, a gene can take on many expression states, from no expression to some expression to high expression. It isn’t just on or off. Those intermediate states of expression can have different outcomes compared to low expression and high expression, just like the dial on an analog stereo. That was the point I was making.[quote=“NonlinOrg, post:19, topic:36834”]
What about “DNA not essence of life”? Do you understand the argument?
[/quote]

I understand the flaws in the argument. DNA is the molecule of inheritance. It serves as a template on which RNA and proteins interact. I don’t see how DNA is the “essence of life” since there isn’t any real hierarchy in the cell when it comes to these molecules. RNA and proteins make DNA, so are they the essence of life?