"Junk DNA Theory" opinion

[ssandlin]

Hello, my name is Spencer Sandlin I'm a student at a local community college here in Alabama. I have a theory on Junk DNA that I'd like to run by you guys to see if it has been offered and also what you think on the subject so here goes.

I came up with this idea when I took basic biology at Wallace and my teacher didn’t understand it and told me to contact you guys.

 

I believe everything in the human body has a purpose now as to rather or not we understand it is another matter. Everything has a flow so to speak another words if something breaks down in one system it will affect another. I believe that same philosophy is very much so true in regards to our DNA. With the complexity of it, or to me anyways, everything has to work perfectly otherwise abnormalities form. When DNA splits and then comes back together how do we know it’s the same helix and not one from another. Furthermore if it is from another how would it know where and in what order to go. I believe Junk DNA is in fact a coding within the strands themselves communicating as to where and in what order the pairings should take place. I think that it could possibly account for the Trisomy 21 as well. There would have to be a reason it split random yes but deliberate. If the Junk DNA communicated for such an occurrence to take place it would.  Another words a misfire in communication it could be a recessive trait passed down from their parents or much further down the line. This would make sense especially in families where they have two children one of which doesn’t have downs.

 

This is just some of what I discussed with her but all I got was a blank stare and you’re talking over my head. I was curious as to what you guys have to say. I thought about publishing my idea but want more than just the theory itself.

Edited September 25, 2019 by ssandlin

[Dagl1]

I currently do not have the time to answer in depth, but would like to stress that, at least to me, it seems that your fundamental understanding of how DNA works and operates. I would recommend looking for more information and understanding before going off in the speculation direction (not that speculating is bad, but generally; total or at least a lot of understanding comes before new ideas). Additionally, it would be good to use more specific jargon, I presume that by DNA splitting and coming back together you mean unwinding and rewinding by helicase activity, if that is the case, then the reason why we know its the same helix is because, generally, nucleobases (ATCG) bind to their complement (A<>T, C<>G) nucleobase and it is highly unlikely a strand of DNA that is complementary to the just unwound strand is present. 

After rereading your message, you may mean doublestranded breaks? If so, how would non-homologous end joining and homologous recombination fit into your story? 
I am not sure how junk DNA could "account" for Trisomy 21, could you elaborate?
Additionally, how would junk DNA's "code" be communicated, there are of course non-coding RNAs located in parts of the DNA that were, originally, considered "Junk", but I think I can speak for at least a portion of the scientific community by saying that the term "junk DNA" is inaccurate at this point.

If you want to discuss things like this or learn more about it, you can send me a private message and we can have a more interactive talk (as I said before, I feel like the current depth of your knowledge is not adequate for new hypotheses (we don't call them theories) regarding specific functions, but you can of course get there! 

-Dagl

[Phi for All]

9 hours ago, ssandlin said:

I believe everything in the human body has a purpose now as to rather or not we understand it is another matter.

I think this argument is unsophisticated, and doesn't belong in your hypothesis. For instance, there is absolutely no purpose to the path the recurrent laryngeal nerve takes in vertebrates capable of vocalization. It's a short distance from the brain to the voice box, yet the nerve loops down below the heart before going back up to the brain, simply because it got caught there as our original common vertebrate ancestor evolved. The poor giraffe has to carry around an extra 5 meters of nerve.

There are quite a few design flaws that have no purpose. Human eyes are fantastic, but have obviously been adapted from more primitive origins. We could now easily design an eye that overcomes all the individual shortcomings, but the eye had to evolve as a unit. Sometimes that means adaptations are carried over for no purpose other than it would take too many resources to correct them.

8 hours ago, Dagl1 said:

If you want to discuss things like this or learn more about it, you can send me a private message and we can have a more interactive talk

Or better yet, the discussion can take place in this thread and involve even greater levels of interaction and broader opportunities for learning. 

[Dagl1]

My apologies Phi (and to other forum members), I did not mean to stifle discussion, but I feel that, in some cases, learning is better facilitated through direct conversations (I explain X, person responds with how they understand it, but does not completely get it, I explain X in another way, etc.). Secondly, while I personally really like this forum, I feel that especially for new learners, this environment may not make them the most comfortable, which could lead them to not follow up on questions as much as they would like to. Oh and of course the formal nature is a little bit of a barrier (see example below, which I had to heavily edit to remove typos and sentence structure). Nevertheless, I see your point; below are parts of our (ssandlin and me) conversation, I have only copied my own text, out of respect for ssandlin's privacy, and left out some responses as they would reveal specific questions that were asked.

I would like to hear if people have corrections, comments on or additions to my explanations:

_______________________________________________

Enzymes by definition are proteins, there are some RNA-enzymes called ribozymes and DNA-enzymes have been artificially made but are not present/functional (as far as we know) in the human genome; they are called deoxyribozymes. RNA enzymes such as the cores of ribosomes (RNA enzyme = ribozyme) are a lot more functional than DNA, mostly due its chemical structure.

Coding = translation, non-coding DNA is just all DNA that doesn't encode for amino acids (although even when looking at the "coding" DNA not all of it is encoding for amino acids). [editing note: Untranslated regions, introns, promoter regions etc. I could be incorrect but I thought these were all considered “coding”]

[editing note: in response to ssandlin’s comment on “purpose”]: Look up retro transposons, it may give you a new insight in the idea of "purpose". There are whole regulatory systems designed to stop retro transposons from killing us, and they are in our DNA, our bodies just can’t get rid of them (easily)
[editing note: in response to the idea of DNA “doing” things] I don't know of any evidence where DNA functions as an enzyme, however DNA structure does affect things: I saw a paper about something similar (but not really the same) a few days back: https://www.cell.com/cell/fulltext/S0092-8674(19)30952-3
in case your university VPN doesn’t allow you to open this or you don’t have access to one right now:
[editing note: @mods, in case sharing of sci-hub is forbidden, please edit it out, I am not sure what the rules are regarding sci-hub] https://sci-hub.tw/https://www.cell.com/cell/fulltext/S0092-8674(19)30952-3

Proteins are strings of amino acids that fold themselves (and/or with help of other proteins) into functional "machines"; these can range from structural roads/cell skeleton (mircotubuli) to gates (transporters/uniporters), to receptors (things that react to something binding to them and then do something) and enzymes (things that facilitate a specific reaction or set of reactions). Since proteins are a string of amino acids, they are encoded for by the DNA each amino acid is encoded by 1 or several combinations of triplets (ATC ATG TGC AAA etc.)

So a protein is just a string of amino acids, which is encoded for in the DNA with triplets of letters (1 amino acid triplet = codon). You can think of the DNA as the Master blueprint for a building, however each worker/machine requires some blueprint to build anything, so in order to create 20 windows, you would have to give the window-makers the blueprint 1 at the time; that’s A very inefficient and B, what if the blueprint gets damaged? That is why DNA is present within the nucleus, where it is (relatively) safe, and RNA polymerases transcribe the DNA to (messenger RNA (mRNA, there are other types of RNA, but mRNA carries information for protein production). A single blueprint of DNA can make many mRNA's which can then be given to the window-, door- and wall-makers, this mRNA can be spliced (i won’t go into detail, it’s an interesting and important thing to look up though), these mRNA's are then used for the construction of proteins.

DNA is the entire blueprint for the building, a gene encodes for 1 (not entirely true, but that requires knowledge of alternative splicing) protein, which would be any component of the whole building, think a window, or a bolt or the cement of a wall (with other proteins being more regulatory and assisting in the placement of the wall (in case the wall itself does not say: "I have to be placed here and here")) DNA doesn’t DO anything; it’s like a book or blueprint that is read it requires proteins and ribozymes (but just consider those as proteins for now) to be useful. [editing note: I understand that this sentence may be not entirely correct, however I felt like at this stage it is better for one’s understanding than going into minutia]: DNA on its own is inert. 

However there are specific proteins that can read the DNA, other proteins that interpret this reading and produce mRNA, then other proteins which transport the RNA to the place where again other proteins make (translate) the RNA into new strings of amino acids=proteins, which are then moved to a sorting location (Golgi) by proteins and made ready to do their function.

[editing note: same thing applies as before; this is not entirely true and should not be seen as a textbook answer] [In response to the name “Junk DNA”] Yes, so because only a very small % of the DNA encodes for proteins, and we didn’t know of a lot of regulatory functions and/or non-coding RNA, it was seen as useless. But as complexity of organisms (single cell vs. animals for instance) increases, the number of genes does not increase linearly, however the amount (quantity/size) of non-coding DNA does.

A lot of the non-coding DNA can be seen as additional IF-statements (if you are familiar with programming), or conditions which can direct the coding genes for specific moment. A "simple" organism may not have to deal with as many variable conditions as the cells in an animal body. Another example would be: as a business/corporation grows twice as large, it won’t grow twice as many DIFFERENT jobs, but it will require twice (for the sake of this example) as many managers and people that direct the extra workers for newer situations.

But of course in the end these are all analogies or metaphors, once you really understand it, you will be able to distil what is true about such analogies and where they fail to explain how cells truly function.

What I would recommend is start by looking up (Wikipedia and Youtube for now, on Wikipedia, search every word you don't understand and follow every link, eventually it will all fall in place): enzymes, specifically kinases and the MAPKKK pathway, get comfortable with the names and what they do; this eventually leads you to: what a gene is, promoters and transcription factors (which CAN be activated by kinases), from there look up the receptors (GPCR's AND ion-channels) as this will lead back to kinases and then to promoters, and give you a decent idea of how signaling works within cells. The CREB pathway is the one I like the most to go from receptor to gene (pictures are great for pathways).

Then it is time to tackle splicing and alternative splicing; lastly epigenetics, the overhyped thing that's important to just get an idea about: understand Agouti mice and DNA methylation, and understand that histones exist and why (specifically) acetylation leads to increased chances of transcription (by making it easier for TF's to bind promoter regions and facilitating RNAP II). You don’t need to understand what all things such as H3k4 (tri)methylation does, but if you understand the concept of acetylation, then other modifications will be understandable as they are conceptually similar. This will also have introduced you to post-translational modifications.

Remember, all of this is Wikipedia, Youtube videos and Google images, once you are comfortable with these things, then it’s time to start with articles. I personally have a not very popular approach to this (but one that leads to way better understanding down the line IMO): find an article (such as the one I linked, or one about something you find interesting (within this field) and go through it. EVERYTIME you don't understand something, look it up, if there is a reference to a mechanism you don't understand, look up that article and continue with the new article. Then when you find something you don’t get in that article (with a reference), go to the new reference. In the beginning, even with good knowledge of the stuff discussed before, you are looking at probably 20 articles before you can come back to that first paragraph of your first article, and then you may find another 5 or 10, afterwards.

This approach requires a lot of work, but once you have finally finished your first original article, you will understand that specific part of the field well [editor note: More likely they will realise that there is an unbelievable amount they do not understand]. Produce in-depth notes (see pictures), it takes longer, but it WILL save you so much hassle and allows you to look up things, even as you may have forgotten the details (e.g. "Ahh there was something with this protein, quick Ctrl+F and there it is; Oh Ye! That’s what it was).

When I say understand everything from an article, it includes the methods (of course, you don’t need to know the super duper in-depth stuff, but you should be able to look at like (depending on the paper) 70% -100% of the graphs and understand what the graph says (and thus come up with your own interpretation). Don’t get annoyed if you don’t get it, some papers are very difficult and the writers are (sometimes) more busy with doing science than taking the time to explain their results in detail.

Attempt to get a good feeling of what was done, why and what it means; basically, interpret for yourself, don’t just get told what you should see, but find out if you agree or disagree with the conclusions of the authors. This requires basic understanding of how (mechanically) the methods work.

Lastly understand the basics of P-values (what they mean and what they don’t mean. P<0.05 is NOT the be all end all) and T-tests/ANOVA. I can help you with it as it’s a subject that’s even for a lot of senior scientists not well understood).

[editing note: this last part is directed towards ssandlin, but goes for anyone] During your reading, feel free to explain what you have learned, ask for feedback, questions or whatever, but do try to find answers yourself first; and when asking questions, do so by explaining what you think and what the consequences of your line of thought are (and thus, lead you to the point where your thinking and whatever a source says don’t logically match, that way you get a good feel for the problem (instead of : I DONT GET IT) and I [other people] can help you more easily).

Picture 1: notes from a long time ago (in my opinion bad notes).

Picture 2: notes I make nowadays (good/better IMO).

 -Dagl 

 

Edited September 26, 2019 by Dagl1