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New Causes of Autism Found in Noncoding DNA

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Re: New Causes of Autism Found in Noncoding DNA

#51

Non-biologist here. It would seem to reason that since non-coding DNA has a role in RNA manufacturing, it would be susceptible to resonance from specific energy signals that would invoke its expression, effectively appending new information to RNA. Once propagated that information made be difficult to subdue. Maybe an analogy is an unexpected object being written to a pubsub topic. Each consumer may have different si…

This is what my thesis is about (I titled it "Rehabilitating Junk DNA"). It isn't that complicated. Your resonance comment is gibberish, sorry. The DNA is a giant tape in base 4 (ATGC). There are programs written at random places on the tape that in a 64 bit encoding (i.e. triplets of quaternary bits). This is "coding sequence", about 1% of the genome (itself 3 gigabases, so 30 Mbases of coding sequence). A tape head (polymerase) comes and reads these out into RNA. The RNA is like a flash copy that is sent to a compiler (ribosome) that translates it into a working protein molecule (a sequence of 20 amino acids with the mapping encoded in base 64, see "genetic code"). There are control sequences proximal (~within 30k bases) to each program that tell the tape head when and how much to read each program into flash (i.e., transcribe RNA). These control sequences are in the 99% non-coding part of the genome. In my thesis i estimated about another 1% is actual control sequence. The rest may be random noise, we'll see.

Re: New Causes of Autism Found in Noncoding DNA

#52

Non-biologist here. It would seem to reason that since non-coding DNA has a role in RNA manufacturing, it would be susceptible to resonance from specific energy signals that would invoke its expression, effectively appending new information to RNA. Once propagated that information made be difficult to subdue. Maybe an analogy is an unexpected object being written to a pubsub topic. Each consumer may have different si…

A simpler and perhaps more useful way of thinking of non coding DNA is to use analogy of a recipe. Coding DNA tells you the ingredients used, noncoding tells you when and how to use those ingredients. Both are essential to proper gene regulation, but one is much harder to study.

Re: New Causes of Autism Found in Noncoding DNA

#53
post #31

With the drastically increased prevalence (which improved or over diagnosis cannot account for) we must look for environmental triggers or factors. Gene changes simply do not happen this quickly. To be clear, I am not dismissing looking for genes, but there are many diseases which are environmental in cause but can be exasperated by a wide variety of genes, i.e. for which we would not attribute the cause to genes/a s…

> which improved or over diagnosis cannot account for

It is often cited as exactly the reason, and appears to be the scientific consensus. In fact you can see large swings in diagnosis numbers based on socioeconomic factors[0], which definitely hints at diagnostic bias.

> The reported increase is largely attributable to changes in diagnostic practices, referral patterns, availability of services, age at diagnosis, and public awareness.[1][2][3] A widely cited 2002 pilot study concluded that the observed increase in autism in California cannot be explained by changes in diagnostic criteria, but a 2006 analysis found that special education data poorly measured prevalence because so many cases were undiagnosed, and that the 1994–2003 U.S. increase was associated with declines in other diagnostic categories, indicating that diagnostic substitution had occurred.

https://en.wikipedia.org/wiki/Epidemiology_of_autism

[0] https://www.healthline.com/health-news/the-big-reason-autism...

[1] https://www.ncbi.nlm.nih.gov/pubmed/17367287

[2] https://www.ncbi.nlm.nih.gov/pubmed/15858952

[3] https://onlinelibrary.wiley.com/doi/abs/10.1002/mrdd.10029

Re: New Causes of Autism Found in Noncoding DNA

#54
post #47

Non-biologist here. It would seem to reason that since non-coding DNA has a role in RNA manufacturing, it would be susceptible to resonance from specific energy signals that would invoke its expression, effectively appending new information to RNA. Once propagated that information made be difficult to subdue. Maybe an analogy is an unexpected object being written to a pubsub topic. Each consumer may have different si…

resonance from specific energy signals Did you have something more specific in mind?

Unfortunately no. The article and other literature I could find in my recent googling suggested that free radicals may have something to do with it, but more generally it seems that gene expression is often conditional. Some genetic markers go expressed in some but not in others. Some only express under conditions of chronic stress or specific toxins. The only thing you might be able to say is that merely having information in your genome doesn’t guarantee it will ever be used, but what causes it to be used varies per circumstances that may vary for each type.

Re: New Causes of Autism Found in Noncoding DNA

#55
post #45
post #41

Earlier quoted context omitted.

Evolution is not a process of finding a global optimum, just a local one. And traits which have no impact on the chance for a species to reproduce just get carried along for the ride. An obvious example of this is the Laryngeal nerve. Fish evolved with this nerve being a simple straight line between the brain and larynx. However, in animals which evolved from fish and have necks, we see that the nerve is "trapped" un…

Sure, I even made this point when I pointed out that the appendix has gotten carried along for the ride in another comment. Do you really believe that 75-98.8% of our DNA serves no purpose and is being carried along for the ride? That doesn't seem like a small inefficiency.

Why would you assume a high grade of efficiency, let alone perfection?

Re: New Causes of Autism Found in Noncoding DNA

#56
post #47

Earlier quoted context omitted.

resonance from specific energy signals Did you have something more specific in mind?

Unfortunately no. The article and other literature I could find in my recent googling suggested that free radicals may have something to do with it, but more generally it seems that gene expression is often conditional. Some genetic markers go expressed in some but not in others. Some only express under conditions of chronic stress or specific toxins. The only thing you might be able to say is that merely having info…

I’ll also add that I mean “resonance from specific energy signals” in the most general sense possible, not ‘quantum woo woo’. Like a lock opening when a matching key is inserted and rotated. You want the lock to open with means motion; resonance is motion in response to specific energy, not general energy. It may be awkward to refer to the ridges of a key as energy, but it is in an abstract and absolute sense. My only formal training is in acoustics to that’s part of my lexicon.

Re: New Causes of Autism Found in Noncoding DNA

#57

Non-biologist here. It would seem to reason that since non-coding DNA has a role in RNA manufacturing, it would be susceptible to resonance from specific energy signals that would invoke its expression, effectively appending new information to RNA. Once propagated that information made be difficult to subdue. Maybe an analogy is an unexpected object being written to a pubsub topic. Each consumer may have different si…

This is what my thesis is about (I titled it "Rehabilitating Junk DNA"). It isn't that complicated. Your resonance comment is gibberish, sorry. The DNA is a giant tape in base 4 (ATGC). There are programs written at random places on the tape that in a 64 bit encoding (i.e. triplets of quaternary bits). This is "coding sequence", about 1% of the genome (itself 3 gigabases, so 30 Mbases of coding sequence). A tape head…

Fascinating, thanks for breaking it down into data structures.

Re: New Causes of Autism Found in Noncoding DNA

#58
post #55
post #45

Earlier quoted context omitted.

Sure, I even made this point when I pointed out that the appendix has gotten carried along for the ride in another comment. Do you really believe that 75-98.8% of our DNA serves no purpose and is being carried along for the ride? That doesn't seem like a small inefficiency.

Why would you assume a high grade of efficiency, let alone perfection?

I’m assuming more than 2% efficiency would be achieved. I could be wrong but why would I assume that when most other systems in the body are massively more efficient that DNA would be the outlier?

Re: New Causes of Autism Found in Noncoding DNA

#59
post #43
post #12

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them? /end venting

Personally I think it's both naive and arrogant to assume that because something is called "junk DNA", that means that the scientific community as a whole have decided to never consider whether it has any impact. There are all sorts of weird terms-of-art in science and I find it quite frustrating that armchair-scientists think they know better purely based on the words that happen to be used.

Maybe my wording wasn’t clear. I never implied that everyone is ignoring non coding DNA. My point was that it seems naive or arrogant to label something as “not useful” rather than “use unknown”. It makes it less likely that a larger amount of people will investigate it.

I think you should also use some data to back up your point because it’s my understanding that the majority of DNA sequencing ignores non coding DNA and the article makes the same point. You also have no idea what field I work in so I’d suggest perhaps asking before coming to the conclusion without any data.

Re: New Causes of Autism Found in Noncoding DNA

#60
post #12

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them? /end venting

The word junk does not appear in this paper. They talk about noncoding regions, noncoding mutations, and noncoding genome.

More generally, the term "junk DNA" was coined to refer to a specific type of noncoding DNA. These two articles give the historical background for the term:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014423/

https://judgestarling.tumblr.com/post/64504735261/the-origin...

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