some types of diets seem to help with autism as well as a few antibiotics which seems to me - as a non scientist - that it might have to do with gut bacteria as well.
anecdotal evidence: http://meatheals.com/category/autism/ in the last one, the 5yo started speaking after diet switch
New Causes of Autism Found in Noncoding DNA
91–100 of 132 posts
Re: New Causes of Autism Found in Noncoding DNA
#92Earlier quoted context omitted.
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.
I broadly agree with your point but careful when saying “no obvious phenotype”. As my former boss likes to say about work in C. elegans: “Worms can’t talk. They seem healthy but maybe they’re extremely unhappy.” Less flippantly, we know that biological systems in general have huge plasticity to buffer environmental changes. The environment is controlled under lab conditions, so loss of robustness due to genetic changes will almost never be detected. We have no good estimate — not even a ballpark! — of how many of these 95 “no obvious phenotype” cases actually have no phenotype, and beliefs widely vary.
Re: New Causes of Autism Found in Noncoding DNA
#93Stupid 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?
It does, genes are translated into protein products that affect cell operation. The relative concentration of these gene>protein products also impacts how a cell operates. How efficiently genes are turned into proteins is determined by quite a few things, but one of them is definitely based on location. Upstream and downstream transcription factors will impact how many copies of a genes proteins are created.
You could broaden your definition of gene to include proximal regulatory elements. If you take that unit and translocate it the answer is much less obvious.
Re: New Causes of Autism Found in Noncoding DNA
#94some types of diets seem to help with autism as well as a few antibiotics which seems to me - as a non scientist - that it might have to do with gut bacteria as well. anecdotal evidence: http://meatheals.com/category/autism/ in the last one, the 5yo started speaking after diet switch
> some types of diets seem to help with autism
Sorry, the actual evidence for this is essential nil. The anecdotes are all explainable by confirmation bias. https://skeptics.stackexchange.com/a/43957/82
Re: New Causes of Autism Found in Noncoding DNA
#95Would 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?
> Would this mean gene-therapy could potentially undo autism?
One of the "autisms", possibly - but it's a long long way before that happens.
> Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing
[citation needed]
Re: New Causes of Autism Found in Noncoding DNA
#96some types of diets seem to help with autism as well as a few antibiotics which seems to me - as a non scientist - that it might have to do with gut bacteria as well. anecdotal evidence: http://meatheals.com/category/autism/ in the last one, the 5yo started speaking after diet switch
This theory doesn't stand in face of science. However: some autistic people have food allergies and comorbid metabolic problems; addressing those will usually alleviate suffering-caused problematic behaviors, and thus make communication easier. This doesn't mean it was "autism treatment" or "autism diet"; you'd get the same effect if you treated a toothache in a nonverbal autistic child.
Re: New Causes of Autism Found in Noncoding DNA
#97Would 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?
Also note that most of these are spontaneous mutations, and that this paper doesn’t distinguish between correlation and causation.
My take, this shoes that something is broken it the very mechanism of DNA replication, expression, DNA repair and cell differentiation, but somehow we fail to detect those aberrant genes on late stage. So their regulation in the early development stages is when we need to look, but that’s very tough to do.
Re: New Causes of Autism Found in Noncoding DNA
#98Earlier quoted context omitted.
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...
Agreed, maybe I misspoke but I wasn’t aware of any place I said it did. “Junk DNA” is a well accepted term by the scientific community and public. https://www.scientificamerican.com/article/what-is-junk-dna-... Humorous take on my point: https://www.amazon.com/Junk-DNA-Journey-Through-Matter/dp/02... I think my main point was missed which is: “labeling something as non useful and leaving it out of the majority of DNA…
> labeling something as non useful and leaving it out of the majority of DNA sequencing as a result has made large swathes of the scientific community unaware of how non coding DNA works within the DNA ecosystem
This is simply not true. Noncoding RNA and in particular regulatory regions have been known and studied for many decades. The reason we know less about them than about genes has multiple reasons, foremost the difficulty in studying them (large-scale studies have only recently become possible). But it has nothing to do with “ignorance”, or with the label “junk DNA” (the SciAm article you link to is utterly wrong to claim otherwise).
Furthermore, although I also think the name has issues (but mostly in science communication), scientists don’t just “assume” that intergenic, non-regulatory DNA regions are unimportant. They have good reasons, backed by evidence, to think so. I’m actually in the camp that thinks that stochastic biochemical function is potentially important (and I used to study repeat elements) but even so there’s almost certainly very little “exciting … unknown science” in junk DNA.
Re: New Causes of Autism Found in Noncoding DNA
#99Earlier quoted context omitted.
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.
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” selection) because mutating it is almost always bad for the individual. What has changed is twofold:
* We have a better handle on what constitutes noncoding, non-junk DNA. The proportion of DNA thus labelled has grown slightly (but only slightly!). We were always aware of its existence but we previously couldn’t study it easily. There are very good reasons to think that the proportion won’t grow much further. The rest is still junk DNA.
* We know more about how new genetic function can evolve using the raw genetic material in junk DNA, and how junk DNA might interfere with the proper function of cells, in particular in the presence of pathogens. But, again, the principle of this was already known (or, partially, at least strongly suspected) decades ago. It was just not studied, and we’re now able to study it better.
But our fundamental understanding of junk DNA hasn’t changed.
Re: New Causes of Autism Found in Noncoding DNA
#100Earlier quoted context omitted.
assortative mating - a certain 'type' of person going to college and meeting people they reproduce with - is also implicated.
Was this the polite way of saying "older, smart people"? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927579/ (Autism As a Disorder of High Intelligence [2016]) > The hypothesis that autism risk in offspring is positively associated with high parental intelligence, and high socioeconomic status, traces to Kanner (1943, p. 248), who stated, referring to autistic children, that “they all come of highly intelligent fam…
These also are groups with more access to health care. Do the numbers factor such effects?