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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

#121

Post by [deleted] »

jballanc wrote: post #6
781 wrote: post #2

Stupid question from a noob: does gene location on a chromosome matter? If I swap gene A from chromosome 1 with gene B from chromosome 2, will this in general keep the cell viable and working the same way?

Gene location is extremely consequential, especially in Eukaryotes (everything that's not bacteria or bugs living near hydrothemal vents). A couple of things that are influenced by position: * First, and most immediate, are promoter/suppressor sequences. These are the bits of non-coding DNA that regulate when a gene is turned on or off. If you move a gene away from its promoter, it will not turn on and off at the rig…

[deleted]

Re: New Causes of Autism Found in Noncoding DNA

#122

Post by klmr »

astazangasta wrote: post #118
klmr wrote: post #89

Earlier quoted context omitted.

Nice explanation but you seem to be saying that at most 3% (being generous) of DNA would be functional (if the rest is “random noise”). This number is over twice as small as the lowest estimate (~ 8%) of even the most fervent critics of ENCODE’s number. I’d love to hear a brief break-down of your reasons, if possible.

Eh, I graduated in 2008. ENCODE was only a pilot yet. We didn't know about lincRNAs. My estimate was based on multi-species sequence alignments so it is pretty conservative. At the time it was not, however; it was doubling the amount of functional sequence. To be honest i am not sure what the current best estimates are based on (i switched fields). 8% seems absurdly high to me, but there is a ton more evidence now th…

Ah, I misunderstood your commend as saying that you’re currently working on the thesis.

Re: New Causes of Autism Found in Noncoding DNA

#123

Post by fragmede »

efa wrote: post #105
hannob wrote: post #82

Earlier quoted context omitted.

> since I believe it's now actually agreed upon that autism rates actually ARE increasing why do you believe that? I'm not aware of any recent research that would point in that direction and disprove the very plausible hypothesis that the increase is an effect of changing diagnosis criteria and increased attention for the topic.

Yes, I'd like to know where you are getting that the actual rates are increasing. My wife and I (parent's of a daughter with autism) laugh how every year they claim the numbers increase - 1/100, then 1/50, etc. These are numbers marketed by Autism Speaks and other organizations to make autism appear more wide spread and increase their funding. This does nothing but hurt people with more severe autism. Widening the ne…

> Widening the net so wide so that any social difficulties is considered autism

That's an oversimplification of the situation, both the autism spectrum (including the now-reclassified Aspergers), and the entire rest of the DSM. Some of those mental disorders also result in social difficulties.

I'm sure you would like more help for only "deserving", specific children like yours, but increased access means more schools that are able to handle IEPs, more teachers able to cope with special needs children, more understanding by all that yelling at a non-verbal stimming child is counterproductive, It means more attention paid by society, more research into the problem, resulting in figuring out the causes of autism.

It really is a spectrum, and limiting help and research to only individuals to non-verbal, body-rocking, non-stop stimming makes it very hard for research to progress - those individuals are very difficult to communicate with! Someone who's limits of communication is PEC cards, is not able to give any useful sort of description of how a particular medication is affecting them.

We are starting to recognize that it is, as least partially, an anxiety disorder, of which we already have a number of doctor prescribed medications, with anecdotal successful treatment for autism.

(I proffer no opinion on Autism Speaks here.)

Re: New Causes of Autism Found in Noncoding DNA

#124

Post by refurb »

klmr wrote: post #99
refurb wrote: post #48

Earlier quoted context omitted.

Actually, “junk DNA” was assumed to have no function decades ago. That’s why it got the name. That’s what I was taught in college 15 years ago. Subsequently it was discovered it does have a very important function. Scientific understanding evolves.

What you were taught in college 15 years ago is still correct. Junk DNA does not have “a very important function”. The “subsequent discoveries” were, by and large, just a failure in science communication. Junk DNA is still non-functional, very little has changed. We know this because it’s not preserved evolutionarily. By contrast, “important” DNA is preserved from mutation (this is called “negative” or “purifying” se…

Many noncoding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of noncoding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these noncoding regions are under strong evolutionary pressure and positive selection.[47] For example, in the genomes of humans and mice, which diverged from a common ancestor 65–75 million years ago, protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented in noncoding regions.[48]

Re: New Causes of Autism Found in Noncoding DNA

#125

Post by wolfgke »

empath75 wrote: post #119
wolfgke wrote: post #111

Earlier quoted context omitted.

> 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. A counterthesis based on personal observations: let us assume that there exists a genetic reason for ASD (plausible), assume that ASD people tend to work in specific jobs in specific branch of the econ…

This is the kind of thing you could test without just spinning out a just-so story.

> This is the kind of thing you could test without just spinning out a just-so story.

Scientists could test it, but I surely do not have the capacity and capability to do so.

Re: New Causes of Autism Found in Noncoding DNA

#126

Post by tathougies »

joshgel wrote: post #19
tathougies wrote: post #10

Earlier quoted context omitted.

Yes, but it's dependent on a lot of things. Some chromosomal areas are more important than others. In humans and other mammals, it also matters from which parent the DNA came from (paternal DNA is different from maternal DNA, but a woman will 'rewrite' her father's chromosomes when passing it on to her child and a man his mother's, etc). Any variation in these things could cause developmental disabilities. However, t…

Sorry this isn't accurate at all. We don't 'rewrite' any chromosomes. Sometimes during errors in replication changes occur, but these are random. They presumably happen approximately equally in both parents contribution to your DNA (though I don't know this to be 100% confirmed empirically).

Imprinting is a thing, and yes, the sex of the parent matters. A woman does not pass on a male imprinted version of her father's chromosomes. She passes on the female version. While methylation is not part of the 'genetic code', it is part of the DNA molecule, and it does impact genetic expression.

Anyway, in your pseudo-scientific world, how do you explain Angelman and Prader-Willi syndrome? Please... the world must know.

Re: New Causes of Autism Found in Noncoding DNA

#127

Post by efa »

fragmede wrote: post #123
efa wrote: post #105

Earlier quoted context omitted.

Yes, I'd like to know where you are getting that the actual rates are increasing. My wife and I (parent's of a daughter with autism) laugh how every year they claim the numbers increase - 1/100, then 1/50, etc. These are numbers marketed by Autism Speaks and other organizations to make autism appear more wide spread and increase their funding. This does nothing but hurt people with more severe autism. Widening the ne…

> Widening the net so wide so that any social difficulties is considered autism That's an oversimplification of the situation, both the autism spectrum (including the now-reclassified Aspergers), and the entire rest of the DSM. Some of those mental disorders also result in social difficulties. I'm sure you would like more help for only "deserving", specific children like yours, but increased access means more schools…

I'm not sure what you mean by increased access. The public school system has very limited funds and personnel. There are some schools with no dedicated reading specialist for example (ever fewer have occupational therapist or autism specialist trained in ABA or other methods). In the real world you have to make decisions on what kids need extra help. It would be great to say everyone gets it but that's not feasible.

I'm all for researching across the spectrum and more public awareness.

Re: New Causes of Autism Found in Noncoding DNA

#128

Post by efa »

alexandercrohde wrote: post #120
efa wrote: post #105

Earlier quoted context omitted.

Yes, I'd like to know where you are getting that the actual rates are increasing. My wife and I (parent's of a daughter with autism) laugh how every year they claim the numbers increase - 1/100, then 1/50, etc. These are numbers marketed by Autism Speaks and other organizations to make autism appear more wide spread and increase their funding. This does nothing but hurt people with more severe autism. Widening the ne…

Let's separate facts from feelings. At the end of the day it really is irrelevant what indirect emotional consequences the facts have, all that matters is that we get the ones that happen to be true so that we can make the best choices going forward. I'll try to find the sources and post them on parent.

How am I expressing feelings and not facts?

Re: New Causes of Autism Found in Noncoding DNA

#129

Post by alexandercrohde »

efa wrote: post #105
hannob wrote: post #82

Earlier quoted context omitted.

> since I believe it's now actually agreed upon that autism rates actually ARE increasing why do you believe that? I'm not aware of any recent research that would point in that direction and disprove the very plausible hypothesis that the increase is an effect of changing diagnosis criteria and increased attention for the topic.

Yes, I'd like to know where you are getting that the actual rates are increasing. My wife and I (parent's of a daughter with autism) laugh how every year they claim the numbers increase - 1/100, then 1/50, etc. These are numbers marketed by Autism Speaks and other organizations to make autism appear more wide spread and increase their funding. This does nothing but hurt people with more severe autism. Widening the ne…

Methodology: type "autism incidence" into google scholar, filter by articles since 2015 and read some on the first page.

Conclusion: It's still pretty-well ambiguous as far as I can tell. You're right that it's not conclusively increasing.

https://link.springer.com/article/10.1007/s10803-018-3834-0 -- Says true autism rates increased between '85 and '98, but since then only diagnosis of autism has been increasing til '04.

https://www.cambridge.org/core/journals/bjpsych-open/article...

I note that I think it's also pretty well-agreed upon that rates don't match up between countries.

Re: New Causes of Autism Found in Noncoding DNA

#130

Post by klmr »

refurb wrote: post #124
klmr wrote: post #99

Earlier quoted context omitted.

What you were taught in college 15 years ago is still correct. Junk DNA does not have “a very important function”. The “subsequent discoveries” were, by and large, just a failure in science communication. Junk DNA is still non-functional, very little has changed. We know this because it’s not preserved evolutionarily. By contrast, “important” DNA is preserved from mutation (this is called “negative” or “purifying” se…

Many noncoding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of noncoding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these noncoding regions are under strong evolutionary pressure and positive selection.[47] For example, in the genomes of humans and mice, which diverged from a co…

Noncoding DNA ≠ junk DNA! In fact, the latter is a subset of the former. Confusing the two is understandable since even scientists occasionally play fast and loose with the terms but scientists nevertheless understand that they are different. To cite from the same article you’ve cited:

> When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA".

And this is by no means a new discovery, functional noncoding DNA has been known for as long as junk DNA.

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