Charles Denault III

The 2nd law basically states that the entropy of a system never decreases or remains constant. Or rather it can never become more organized, or less disordered.

Yet nature has been churning out more and more complex organisms for the past few billion years, so what’s going on here? How can a system (in a slightly different sense of the word) become more complex? How can humans have evolved from simple bacteria? Wouldn’t it make sense that humans would be devolving?

Nature does amazing things. When you look at the genomes of both humans and simple bacteria, you find something amazing. Even though humans are far more evolved, their DNA has been shrinking in a sense. There’s some single celled organisms with genome sizes far larger than the human genome. I believe this is because nature is obeying the 2nd law. It’s continually decreasing disorder.

The first organism to gain a genome, most likely some exotic form of a single celled guy or a virus, probably had built a genome much, much larger than currently exists. The vast majority of the DNA didn’t do a thing, not because it didn’t code for anything, but because the cell didn’t have anything to do with it. It hadn’t yet built the necessary organelles and enzymes. It was the simplest of everything.

The cell began to increase in complexity. The only way to do this, without violating the laws of the universe, is to allow the DNA to increase entropy. This is where the magic happens. When the cell increases entropy, or increases disorder, it subsequently increases efficiency. What better way to progress evolution? Abide by laws that should break systems down, whilst secretly building more complex machines. All by accident. They’re rebels, in a way.

It makes perfect sense too. Imagine the possibilities that could stem from random mutations throughout a near infinite number of organisms over the past 4 billion years. Combine this with DNA uptake systems and suddenly you have a rapidly evolving, however random, set of organisms. All fighting the second law of thermodynamics, mostly losing, but the lucky ones survive to reproduce and push the species forward.

Do this long enough and you wind up with a human. The pinnacle of evolution.The organism destined to get to know the universe.

I was reluctant in choosing a suitable title for this post…

When I watch my dog or cat navigate through the house with perfect precision, I can’t help but wonder. What’s going on inside their heads? I’ve narrowed it down to two possibilites. It’s either muscle memory from countless repetitions or they have the ability to draw the floor plan in their minds, similar to humans. But even for me, it’s tough to produce a two dimensional picture of the floor plan of a house in my mind. Instead, I can visually think my way through. I can imagine that I’m walking out of my room and taking a left down the hallway, where I take a right into the living room. I pass the couch to my left, with artwork to my right. I can’t tell you the number of steps I need to take, but I can think it through in my mind. I believe the animals are doing the exact same thing.

I’m a somewhat experienced hunter, having been sitting in the woods every season since I was just 10 years old. I’ve come to know a fair amount about the patterns of the animals, most notably deer. They have intricate trail systems spanning for miles upon miles through the woods. Trails that the average person wouldn’t even recognize as they’re so complex. Yet the deer don’t just make new trails whenever, they follow the existing ones. We frequently create new trails with our 8 wheeler out through the swamps. We do it every two years or so, to keep the vegetation in a constant cycle so we don’t destroy the land. Every time we create a new trail, there is countless deer sign (prints, rubs, scrapes, poop) up and down it. They’ll follow the trail, probably because it’s just easy walking, but it’s the fact that they use the trails that caught my curiosity.

If we don’t create a new trail, neither do they (assuming that there aren’t any other significant changes to the woods). So here’s miles of trails that the deer systematically, and predictably, follow throughout the year. They’re not randomly walking these trails, which means that they have to be doing the exact same thing that we do when we walk the floor plan of our house.

It makes sense that other animals would be able to do such similar things with their mind. It’s necessary for survival. Imagine the animals that couldn’t remember their way back to safety. Don’t you think natural selection would have killed these off very early? Of course.

I think that the difference between their minds and ours is very little. If anything, it was only our body that enabled us to rise to where we are today. Had we not developed the capabilities to vocalize, use our opposable thumbs, etc. our brains would be little use to us. Passing down the acquired knowledge and skills would be infinitely harder (although we frequently see this, for instance in crows which was recently discussed at TED). It’s almost as if our brain is capable of nearly anything, it’s just waiting for the necessary mechanical pieces to finish the puzzle. Evidence of this might be shown in the latest experiments with animals and humans controlling computers using thoughts. The monkey with the robotic arm is exceptionally eye-opening. So isn’t it possible that the brain size is directly proportional to the complexity of the body? Obviously, as you look at various animals their respective brains change in size with their body size.

My apologies if this is dated or debunked. I’m just thinking out loud.

A little thought I had while bear hunting in Canada.

I’m not too sure of the implications of this, nor do I know if there is a need… Hell, I don’t even know if it’s even remotely possible.

Here it goes:

You can take a piece of DNA that codes for a protein. You can then break it down into the specific amino acid. That’s pretty self explanatory. We’ve been doing that for years now. Then you know the specific order of the amino acids. You officially have the primary structure of the protein that is being coded.

Then, using a “cheat sheet” of sorts, you could determine whether the amino acids form an alpha helix or a pleated sheet when they’re linked with hydrogen bonds. You now have the secondary structure. Repeat this process until you determine the tertiary and quaternary structures.

We already know the exact structure of many proteins, so assuming the amino acids follow the same rules when they fold. A comprehensive database can be formed to describe the specific folding, linkage, etc. A simple program could easily render the structure, allowing us to easily view the entire structure. Whether or not this is already being done, I’m not too sure… but I thought it might be neat. Who knows what sort of implications this could have, perhaps it would be the first step in visualizing more complex interactions between proteins, organelles, cells, tissues! Who knows! After all, I do believe that there is a pattern beneath everything and every organism on this planet is just a set of instructions.

Since the dawn of computers, scientists have longed to bring intelligence and consciousness to their computers. Countless attempts at beating the turing test, machines that can play chess, natural speech interpreters; it’s all a collection of algorithms written by a human trying to play God. Functions with specific arguments, designed to return an even more specific result. This sort of system can never yield anything other than a pure computation machine.

Biologists hardly understand the systems that make humans tick. It was only recently that “junk DNA” turned out to do something after-all. The electrical signals from the brain can be monitored endlessly, however the neuroscientist still cannot produce a picture of the cognitive canvas. They claim modern marvels by designing robotics that interface with brain, yet the true mystery is the brains elasticity and willingness to accept and control such devices, not their primitive technology.

I believe that computers are bound to go through phases, just as any other technology has done. Much alike the hand mill/steam mill example, the present day computer is not the pinnacle of technology, but merely an extremely basic version of what’s to come. Quantum computing will be the logical next step. The proposed computing power of such a machine would be unparalleled by today’s technology. Quantum computing, however, will be replaced. I believe that the ideal design lies within that of biological processes.

First, we must learn to understand the system. It will start with a primitive organism, such as a bacteria. The genome of the species will be fully documented, and programmable. Geneticists will be able to “code” for new genes, producing miraculous results. DNA will become the ultimate programming language, much like assembly for computers.

Scientists will then learn to utilize such protocols as chemotaxis and photosynthesis, one of the most elementary functions of these bacteria. More about DNA will slowly become understood, and the miracles of birth will be recorded in a clear and concise manor, easily reproduced.

Soon everything regarding biological species will be understood. From the way humans think, to the subtle differences between man and dog.

I believe that geneticists will uncover a higher level programming language embedded within the DNA. I believe that this language is going to be found within the non-coding regions of the genome, which was largely regarded as “junk.” It’s going to be at least a decade before it’s truly understood, and perhaps an additional decade before the conceited scientists realize they made numerous mistakes and misconceptions the first time around.

If computers have taught us anything, it may be that hardware is the structure for which everything is built, but the true innovation lies within the software. Even still, the software may have numerous levels. For instance, everything is ultimately built on a set of processor instructions, which then the operating system interacts, on top of which the programs run. For a system as elastic as the brain, which can lose ½ of it’s mass and still function perfectly, it wouldn’t make much sense that everything would be written in the lowest level language.

The brain structure has to stem from instructions within the DNA. Yet imagine if the coding regions of the DNA are merely construction instructions, while the operating portion resides within the noncoding region. The noncoding region is actually a cryptic structure which defines the very algorithms that control every process within the organism. This would also solve the age old question as to why the DNA of a chimp closely (98.something%) resembles that of a human, and a banana has somewhere around 50 % of similar DNA.  It’s because each organism, regardless of its structure, behaves and acts the exact same. All of this did, theoretically, extend from one single organism way back when… when the first cell adopted viral DNA! They’re all operating on very similar instructions, adding further validity that animals are not so different than you and I. (Assuming you’re human)

Deoxyribonucleic acid, more commonly known by its acronym DNA, is the fundamental code that makes up the human body, and all other life forms on the Earth. Before I dive into my little analogy, let me give you the specifics on what DNA is.

DNA is a polymer, which is composed of monomers called nucleotides. The nucleotide consists of a 5-carbon sugar, a nitrogen containing base, and a phosphate group. The DNA consists of four different types of nucleotides, which differ only in the nitrogenous base. The four different nucleotides are represented by the letters A, T, C, G which correlate to adenine, thymine, cytosine, and guanine, respectively. The DNA is organized in two complimentary strands, which form a double-helix shape.

Where does this crazy stuff come from? The easy answer is that it comes from the parents of the critter (or you). So your parents each donate half of their DNA, which combine to create a unique offspring.

So this DNA is contained in a ton of places throughout the cell, but generally every cell in the human body contains a copy of your DNA. It’s stored safely inside the nucleus of the cell. So when something needs to be manufactured inside the cell, a little enzyme comes along and unwinds and unzips the DNA into two separate strands. So this is like the source code for humans.

When we look at computer programming, we generally have two classes of programming languages. Compiled and interpreted. Compiled programs are written using a programming language, such as C++, and are run through a compiler to make a functional program. The compiled program can be reverse engineered or decompiled into the original source code. Interpreted code is written just like any other program, however it’s not compiled. It’s interpreted and then returned each and every time it’s executed.

Now back to the cell…

Inside the nucleus we have some DNA, which then needs to get executed, or translated, into a functional protein or enzyme. The DNA runs into an enzyme which then compiles it transcribes it into a piece of RNA which then will eventually directly code for the protein. So the cell is actually maintaining a copy of the original DNA inside its nucleus at all times. This helps decrease the possibility of “accidents” or mutations. DNA acts like a combination of interpreted and compiled code. It is first interpreted which generates the RNA and then compiled into a protein. To perform a task.

So sure, there’s a copy of all the genetic code lying around in every single cell within every single organism but theres also the product of the entire code — everything within the organism that isn’t DNA. Every piece of an organism was coded by DNA, so why can’t we just break down those pieces? Why can’t we decompile them into the code that made them? Wouldn’t that make understanding organisms so much easier? We could decompile each and every enzyme within the human body, and learn how it’s exactly constructed.

There’s a huge difference between reading code and understanding it. Sure, anyone can look at latin and pronounce the words correctly, but you have to have an advanced understanding of the language to get anything out of it. You need to know not how to say the words, but how to understand their meaning. If we can understand not what each piece of DNA makes, but also how it makes it… we would make a quantum leap of which I can’t even begin to fathom.