New Causes of Autism Found in Noncoding DNA • Hacker News Board

Re: New Causes of Autism Found in Noncoding DNA

#71

Post by dang » Wed, May 29, 2019, 4:55 AM UTC

rockinghigh wrote: post #60

dkoston wrote: 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...

Ok, we'll replace junk with noncoding above.

Re: New Causes of Autism Found in Noncoding DNA

#72

Post by bduerst » Wed, May 29, 2019, 5:10 AM UTC

Retric wrote: post #17

dkoston wrote: 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

Junk DNA means non coding and without benifit. Due to the random nature of mutation such sequences are expected. However, verifying any specific sequence is useless is difficult. One important consideration is sequence length may have value even if the content is meaningless. Another is random sequences may aid long term adaptation even if they don’t currently do anything. So, if anything Junk is a fairly descriptive…

Junk (and/or noncoding) DNA provides necessary structure for our chromosomes, spacing for transcription, and some defensive properties.

There are many benefits beyond just that of coded information storage, which people are focused on here in this thread.

Re: New Causes of Autism Found in Noncoding DNA

#73

Post by jtwebman » Wed, May 29, 2019, 5:36 AM UTC

alexandercrohde wrote: post #23

Would this mean gene-therapy could potentially undo autism? Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing, and not just increased diagnoses, is there any candidate theory as to why mutations would be higher in developed countries recently?

I would think diet

Re: New Causes of Autism Found in Noncoding DNA

#74

Post by lazyasciiart » Wed, May 29, 2019, 6:01 AM UTC

jtwebman wrote: post #73

alexandercrohde wrote: post #23

Would this mean gene-therapy could potentially undo autism? Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing, and not just increased diagnoses, is there any candidate theory as to why mutations would be higher in developed countries recently?

I would think diet

This comment would be more interesting with some kind of source or explanation for your thought.

Re: New Causes of Autism Found in Noncoding DNA

#75

Post by dnautics » Wed, May 29, 2019, 6:02 AM UTC

gravelc wrote: post #67

dnautics wrote: post #29

Earlier quoted context omitted.

I'm going to go against this and say no. We swap gene locations, all the time wholesale in mice, and usually the effect is limited. That doesn't get you a paper, so of course you publish when something... more interesting crops up. It's just that there are many well-studied systems where where there are profound and severe effects that are singly extremely consequential, where you go "huh, wouldn't have guessed that"…

I'm going to disagree with go with 'sometimes yes and sometimes no'. Take a construct and transform it into a plant. Check the expression of the transgene from hundreds of different transformation events, and there'll be huge variation, from highly expressed to silenced, even though all inserted transgenes have the same promoter and terminator. Location matters. However, if the function of gene A is redundant, or it…

I would make a bet. Randomly generate 100 spots in the mouse genome, let's say maybe not in centromeric locations. Don't correct for being inside an ORF or a promoter. Pick 100 random translocations swapping these spots. 95 of them will be viable with no obvious phenotype.

Re: New Causes of Autism Found in Noncoding DNA

#76

Post by dnautics » Wed, May 29, 2019, 6:07 AM UTC

sjg007 wrote: post #61

dnautics wrote: post #29

Earlier quoted context omitted.

I'm going to go against this and say no. We swap gene locations, all the time wholesale in mice, and usually the effect is limited. That doesn't get you a paper, so of course you publish when something... more interesting crops up. It's just that there are many well-studied systems where where there are profound and severe effects that are singly extremely consequential, where you go "huh, wouldn't have guessed that"…

https://www.annualreviews.org/doi/abs/10.1146/annurev-genet-... and https://www.sciencedaily.com/releases/2010/10/101014144312.h...

The second one relates to a feature at the metaorganismal level; namely the evolution rate. Fun fact: human chromosome 1 is the merger of two simian chomosomes and has two centromeres

Re: New Causes of Autism Found in Noncoding DNA

#77

Post by bad_user » Wed, May 29, 2019, 6:09 AM UTC

spraak wrote: 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…

The genes aren’t changing, but the environment is and the modern environment is interacting poorly with our genetic heritage and increasingly so.

Even so, looking at genes and identifying the pieces is still important. For example having a test that determines risk during pregnancy would be awesome.

Re: New Causes of Autism Found in Noncoding DNA

#78

Post by spraak » Wed, May 29, 2019, 6:45 AM UTC

bad_user wrote: post #77

spraak wrote: 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…

The genes aren’t changing, but the environment is and the modern environment is interacting poorly with our genetic heritage and increasingly so. Even so, looking at genes and identifying the pieces is still important. For example having a test that determines risk during pregnancy would be awesome.

Essentially what I'd said, so I agree! I'd like to have more awareness and study of what in the environment is causing it

Re: New Causes of Autism Found in Noncoding DNA

#79

Post by onetimemanytime » Wed, May 29, 2019, 7:05 AM UTC

My guess: older parents + environment. Granted people are having children later in life but that doesn't account for the increase in cases (Better detection and incentives in funding to label kids autistic is another possibility.) So something is now in the air, food or water supply that is making these changes. Maybe older parents are more prone to this?

Re: New Causes of Autism Found in Noncoding DNA

#80

Post by Toine » Wed, May 29, 2019, 7:13 AM UTC

spraak wrote: 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…

I'll put in out there (at the risk of being downvoted) : an extremely destructive/insensitive world around a developing child, as a fetus or later, is to me one of the root causes of autism. See Bruno Bettleheim's theories (refrigerator mother, The Emtpy Fortress, etc).

"Autistic people have the conviction that their efforts have no influence on the world, because in the past they were convinced that the world is insensitive to their reactions."

This comes from my personal experience.