Is Most of Our DNA Garbage?
nytimes.com
nytimes.com
DNA is not merely "data"; to make everything even more complicated, some of it is probably both data and structure... maybe even both at the same time.
That being said I think the basic gist of your comment is correct. It's very old spaghetti code... just hyper dimensional massively parallel spaghetti code.
I'd love to start a project to study this.
At least we're getting to the point where we can flip switches and monitor for changes. Debug print!
Right, because a single cell transforms into a whole animal (horse, giraffe, whatever) and that takes zero information. Really? Somehow I doubt it.
A multicellular organism is a really big, complicated state machine and the "junk" DNA is what's needed in order to go from a single cell to many billions of cells organized in the particular fashion that they are.
To suppose that everything that doesn't directly code for a protein is "junk" is incredibly arrogant; just because you don't currently understand something doesn't mean that it cannot be.
As an engineer I'm guilty of this all the time; something I don't know how to do is impossible but once someone explains to me how to do it, it's trivial. I've had this happen enough times that I can now recognize that my "impossible" isn't necessarily actually impossible, just that it might be impossible to me right now.
Sure it doesn't have an exact template of _precisely_ how to do everything, but there's a lot of information there. Maybe it's not huge relative to the amount of theoretical information DNA contains, but I strongly suspect that the 98% is junk claim will eventually be found to be laughably wrong.
We can sequence DNA, but that raw data isn't something that we can mentally digest very easily at all.
Maintaining these "extra copies" of the genome costs energy (lowering survivability), but you get something very loosely like RAID mirroring allowing the genome to survive more errors. Having more than a single backup copy also allows a single plant species to have a lot more variation, as alternative genotypes can be saved across generations in the "backup copies".
Are flowering plants just written in a language that doesn't have "for loops" so everything is just written out line by line?
http://en.wikipedia.org/wiki/Genome_size#Genome_reduction_in...
http://gbe.oxfordjournals.org/content/early/2015/01/28/gbe.e...
in the two articles I mentioned,I think the way the "offspring" circuit worked in an extremely baffling(complex) way relying in physics in way beyond human design (aka the way the disconnected logic gates were still necessary for functionality) have insight into some of possible complex interactions of dna. They look like unnecessary garbage until you try to remove them and break a ton of stuff.
On average, each baby is born with roughly 100 new mutations.
If every piece of the genome were essential, then many of those
mutations would lead to significant birth defects, with the defects
only multiplying over the course of generations; in less than a
century, the species would become extinct.
So I don't see how NOP padding helps.
My thoughts are this, DNA is not used just for an individual survival but also a mechanism to allow adaptation at some higher level. Like how some deep learning AI's learn how to play games by making random moves and getting feedback from the score changing. For DNA, we get random mutations/moves in the form of transcription,replications errors or Meiosis , and the feedback comes from successful reproduction(surviving to play the game again).
So what we call junk DNA, might actually play a large role in this sort of "learning" mechanism.
I hope I explained that decently. A lot of my thoughts come from this book http://en.wikipedia.org/wiki/The_Selfish_Gene
First mechanism - to go into production you have to pass unit tests (race to the egg). It's only 1 cell, so either it works or not, and if you were the fastest you probably didn't have most of the really bad mutations.
Then after you are in production you run million copies of the code, and to be safe against mutations there's sth like erlang exception handling - if sth's wrong kill the process, start a new one.
The problem is - sometimes the process gets so wrong it doesn't respond to kill signal.
How did they arrive at this conclusion?
The mutations that makes you immobile - the same.
The mutation that mess up with your instincts, and reactions to chemical enzymes - same (you won't go the right way).
And so on.
It's a little like unit testing - it checks all the basic routines.
Telomeres (the HLT HLT HLT HLT HLT... sequence at each end of a chromosome) are pretty well documented. They can be reasonably analogized to those 404 pages with a comment along the lines of
<!-- Your browser won't show you our custom 404 page
unless it beats a size threshold, so just to be sure,
we've put the text of War and Peace in here.
Have a nice day!
[...]
-->
It's also possible that I am misunderstanding how telomeres work.
I guess I also have a hard time figuring out what people are trying to say when they call parts of the genome "junk".
Perhaps what's "junk" is contextually dependent ? One human's trash is another human's treasure ?
The mechanism here isn't a mystery. As I originally pointed out, you'll die when your telomeres are gone from loss of DNA. Every time a cell divides, a certain amount of DNA is lost from the ends of each chromosome. Imagine if every time you copied a file 4 kilobytes were lopped off the beginning and end of both copies. Telomeres are padding (again, they code HLT HLT HLT HLT HLT HLT HLT HLT HLT...) that can be lost without affecting the functioning of the cell.
Some new research papers are emerging that question the existing model we have about telomeres. http://journal.frontiersin.org/article/10.3389/fgene.2015.00...
Quote from that paper "summarizing recent research findings, Trusina (2014) conclude that recently obtained knowledge ‘shift the telomere paradigm from a simple clock counting cell divisions to a more complex process recording the history of stress exposure within a cell lineage.’ "
So I find it reasonable to think that telomeres could be more than just padding, like a clock or history of stress exposure in a cell lineage.
A lot of people expect that at the molecular level life is organized and sensible. But why should that be the case? On the macroscopic level, living organisms are a mess. It is my belief that at the biochemical level the chemical reactions are as organized as the branches on a tree---that the chaotic design of life at the microscopic level mirrors its design at the macroscopic level.
Evolution isn't purely random. There's nothing random about what works and what doesn't. Over time, differential selection and other effects (e.g. sexual selection) work to transfer information about the environment into the genome. Evolution is a learning process. It's just that the representation that it generates is difficult for us linear thinkers to interpret.
It only appears irrational from an anthropocentric point of view. It's not rational to us because we, having brains that work in a certain way, are biased toward seeing things as linear chains of cause and effect. That's how we think and that's how we like to build stuff, but obviously that's not the only way stuff can be built.
For all we know elsewhere in the universe there are beings that think in massively parallel super-holistic causality-matrix terms. To them evolution's designs would seem perfectly rational, while a UML block diagram would seem insane. "Nothing has only one cause or one effect," they would mutter... in a language in which every word implies everything to varying degrees and each syllable of a sentence must be parsed in parallel with all others.
Except of course that evolution comes up with solutions that are so clever and so intricate that we, with all our scientific brains, have barely scratched the surface of understanding it. Now if it acts intelligently, walks intelligently and quacks intelligently, then maybe we should just call it intelligent?
It can be thought of as an alien form of intelligence. It "learns" and "thinks" but not in a human-like way. It does not design things the way we do.
Argumentum ad Lovecraftium: http://lesswrong.com/lw/kr/an_alien_god/
Non-deterministic, yes. Unpredictable, sure. Chaotic... you betcha.
Random... certainly not.
And not irrational - the process is driven to optimize for survival, and selections occur accordingly. It meets the economic and game theory definitions for rational behaviour.
The rationality is not driven by a sentient intelligence, but the result could arguably be called a limited form of intelligence, and we know it can certainly give rise to expressions of intelligent systems.
It is a very nice explanation, shows many similarities, while also making Intercal seem sane.
Not the original article I'm thinking of, but related:
https://www.uam.es/personal_pdi/ciencias/genhum/bibliogenoma...
Having said that, there is some fanboy culture and attachment with science and DNA tinkering. Some "discoveries" and claims sometimes come from such fanboys. People on HN are not different. In fact majority of the comments here signal as coming from fanboys.
Now to the topic of DNA: DNA, if a product of evolution, could not be mostly composed of garbage because nature has its own "garbage collector." Much of the DNA is important and significant in some shape or form. It won't be apparent in a simple experiment, but it may be apparent over a lifetime or maybe over generations.
There is evidence to back this up: a recent NPR show, i forget what, claimed that your grandfather's hunger at the age of 9 influenced your chances of heart attack. This brings up DNA's influence across lifetimes. And the complications are so much deeper.
Our fight to try to understand DNA is incredible. We are not there completely. And maybe this is the longtail part of science. But we will understand it more and more, and imagine the information we extract then. I bet much of it will debunk everything we so arrogantly claim today.
Ah, no, it doesn't. If you think "survival of the fittest" will somehow magically cull non-functional, non-deleterious DNA out of the genome (except by accident), then you don't understand evolution.
It's kind of hypocritical to call others "arrogant" when you're opining on a topic you clearly don't grasp yourself.
Think of DNA as computer code. Think of each creature as a robot with computer code built in. Now think of DNA as also having the code to recreate the creature. Overloaded DNA will collapse. Or incredibly sophisticated biology will be able to handle overloaded DNA. Either way, too much complexity breaks. You may call it "Survival of the fittest" implying chaos theory but I call it harmonious morphology implying benign force.
You are 100% wrong about this. DNA that is not needed does not "wither" away. If it's benign, it'll most likely stick around.
> Overloaded DNA will collapse.
This sentence doesn't make any sense. How do you "overload" DNA? What does "collapsing" look like?
> Either way, too much complexity breaks.
What is "complexity"? Can you measure it? How much is too much? What "breaks", and how?
> You may call it "Survival of the fittest" implying chaos theory
What does chaos theory (roughly, the idea that small changes in initial conditions have dramatic effects) have to do with anything we're discussing?
> but I call it harmonious morphology...
Please define "harmonious" and describe how to measure it.
> ...implying benign force
I suspect you started with benign force and worked your way backwards, ignoring any inconvenient evidence.
Why would it stick around if it is not needed? Why wouldn't it be free to morph if it did not matter? Why wouldn't it change if it did not affect the being? Evidence exists that DNA changes due to stresses in environments, so hereditary (e.g. the parent has it, so the child must) is not sufficient to explain why garbage DNA is still transferring over generations later.
> This sentence doesn't make any sense. How do you "overload" DNA? What does "collapsing" look like? > What is "complexity"?
If a creation of an object relies solely on DNA, then there must be some sort of ignore protocol built into the creation factory for the DNA part that is meaningless. Overloaded DNA has excessive meaningless data. An enormous amount of complexity would be required within the creation factory to handle this overload.
> Chaos theory ... The idea that random changes occur and the only changes that survive are the ones that can still adapt to their environment despite or in spite of the change.
> Please define "harmonious?
Harmonious would mean the very stable and smooth transitions of creatures to change from one to another without there being some sort of "noise" e.g. rapid fluctuations in genes. If creatures can transition uniformly to another creature, why not several different creatures across several different environments (sort of like man-made innovations in isolated environments). Failures and successes would both appear on graphs.
> how to measure harmonious? how to measure complexity?
Measuring harmonious is akin to measuring cold energy. You cannot measure something that does not exist, but instead you measure it by the lack of its opposite. (you measure cold by the lack of heat). Complexity is only apparent when things break. If you don't see things breaking, you cannot witness complexity.
> you started with benign force and worked your way backwards, ignoring any inconvenient evidence.
Actually, its the other way around. A researcher must constantly battle the concept of unknown/benign/hidden/dark energy/force/matter to figure out why things work the way they do. A researcher is always digging, always denying, the concept of an unknown force, in finality to achieve the phrase "That's how!" I call it peace at a certain point. But for a person with an agenda, the inconvenient fact may be that there is an unknown force. Sometimes, these things are cloaked as laws of physics, that some events other than this event just cannot happen. Other times, they are called theories, until they are met with an enigma, where then it is broken.
> Why would it stick around if it is not needed?
WHY WOULDN'T IT??? It's not expensive to carry junk DNA around - it just sits there, not doing anything, not creating proteins, not affecting anything. You're proposing that there's some sort of janitor going through and cleaning up the nonsense and it's just not true. If there is such a mechanism, point to it. Name it. Tell me what it is. Tell me what the evidence of it is. Just link to a wiki page!
I think the problem is that you're stuck on thinking about DNA as procedural program code instead of on its own terms, how it actually operates.
I'll try to explain a few things, in a last ditch attempt to appeal to your intellect:
DNA gets transcribed to mRNA based on START and STOP codons (codons being sequences of three bases). Then the codons in-between START and STOP on the mRNA strand get translated into amino acid chains, also known as proteins. The "ignore protocol", such as it is, is then twofold: 1) if a sequence doesn't occur between START and STOP, it's highly unlikely to ever get transcribed into mRNA, and 2) if an mRNA contains nonsense codons, or its number of base pairs is not divisible by three, then the resulting protein is most likely benign, or at least not harmful enough to prevent the organism from producing offspring and therefore propagating the harmful sequence. (If it is harmful enough to affect reproductive viability, then it doesn't tend to stick around very long.)
Not all DNA does anything. Plenty of it is just hanging on for the ride, not harming anyone, and so not selected against by natural selection.
> I call it peace at a certain point.
I call it giving up the search. Just because you don't understand something doesn't mean you give up trying to understand.