[HN Gopher] The genome diversity of major crops tells the story ...
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The genome diversity of major crops tells the story of their
evolution
Author : PaulHoule
Score : 49 points
Date : 2024-08-01 14:24 UTC (1 days ago)
(HTM) web link (phys.org)
(TXT) w3m dump (phys.org)
| sharpshadow wrote:
| Anbody heard of the Urzeit Code?
|
| https://archive.org/details/der_urzei_code
| PaulHoule wrote:
| How do they apply the field?
|
| There actually are electric fields in nature that can get
| pretty strong sometimes. My undergrad school was New Mexico
| Tech which has a strong atmospheric physics program so one of
| our senior lab projects was
|
| https://en.wikipedia.org/wiki/Field_mill
|
| which demonstrates the principle of turning a DC signal into an
| AC signal which can be more readily measured and introduces the
| powerful
|
| https://en.wikipedia.org/wiki/Lock-in_amplifier
|
| So I have a pretty good picture of how you _measure_
| environmental fields but not how you apply them. Do you put a
| net over the crop and charge that up?
| NotGMan wrote:
| I don't remember the source but in one experiment (some other
| researches) put plant seeds between two strong magnets.
| sharpshadow wrote:
| They applied a static electric field. [1]
|
| 1. https://patentimages.storage.googleapis.com/d9/34/04/33955
| 71... 2. https://patentimages.storage.googleapis.com/1c/60/8d
| /4ddfe08...
| PaulHoule wrote:
| I'd add that the "omics" train has really left the station. It
| seems almost every week I hear about some new species that has
| been sequenced, including crazy polyploid species with huge
| genomes. For that matter it seems that after 20-30 years they
| finally are figuring out the regulatory function of "Junk DNA"
| is. It seems like molecular biology is in a golden age now.
| mjburgess wrote:
| Sure, but much of what has been discovered is that there arent
| "genes for X". The human genome is only 20k genes, 90%+ we
| share with a mouse.
|
| This really sours the whole edifice of 20th C. 'genetic
| statistics' (, heritability, etc.) -- and puts well into light
| the eugenicist origins of frequentist statistics itself, and
| the vast amount of pseudoscience it's given rise to.
|
| Yet, popsci, and many research areas have yet to catch up.
|
| Children are still taught there are such things as dominant
| traits, and genes for eye colour, etc. Yet we've no idea of the
| full genetics of eye colour.
|
| I would say this "golden age" is more a discovery of how
| everything we have previously believed is BS.
| PaulHoule wrote:
| Yeah, I have this 1970 book that I like to copy pictures out
| of
|
| https://mastodon.social/@UP8/112780705488252948
|
| which I think is usually ahead of it's time but the genetics
| unit seems backwards in that it doesn't say a word about
| molbio and has the same experiments were you observe the same
| few phenotypes that are sorta-kinda described by Mendelian
| inheritance, not telling you that those are the only ones,
| that we can't trust Mendel's lab notebook with the peas, etc.
|
| "Personal Genomics" in the sense of 23 and me has been a
| wash. For one thing the SNP approach is limited in what it
| can do, but even if you had a real sequence teasing out the
| personal variation in terms of Genes x Environment can only
| go so far. What's interesting to me about genomics is the
| things that are the same and can be understood to a great
| deal mechanistically such as all of us Eukaryotes sharing a
| common "operating system" in terms of the machinery of
| protein synthesis, cell division and such. Hundreds of genes
| are known that affect diseases such as asthma, diabetes and
| schizophrenia and even if a polygenic risk score is possible
| a doctor is going to give a person with a high risk score the
| same advice as a person with a low risk score and give the
| same tests (fasting glucose, A1C) except maybe he ought to be
| a little more emphatic to the high risk person and the high
| risk person should take it more seriously.
|
| (For that matter my experience with animals leads me to think
| animals are much more the same as us than different even when
| it comes to things like intelligence and communication. My
| belief was confirmed when my stray cat, "Bob B" seemed to
| understand that his path to a better life went through me
| when after 2 1/2 months of stonewalling me he got quite
| articulate in terms of using his "voice" and gestures such as
| pointing at the window and door to indicate he wants to go
| out, pointing at the TV and having an expression that seemed
| like disapproval, etc. I think these behaviors are basically
| intrinsic to mammals and birds if not some reptiles. You can
| certainly learn to communicate with animals better but a lot
| of it is instinctual)
| pfdietz wrote:
| So, if the difference between humans and mice isn't because
| of genetics, what is it due to?
|
| "Genetics" isn't just "protein coding genes". Nor do genomes
| being X% similar mean the organisms must be X% similar.
| mjburgess wrote:
| Well, what explains the climate? The mineral composition of
| the earth? (etc.)
|
| Sure, if that were different, so would be the climate. But
| the climate is severely under-determined by that
| composition -- if you drive it by a different sun, a
| different meteor strike, etc. it would be radically
| different.
|
| Take the same genome and biochemically intervene on the
| conception, pregnancy, development, etc. of an animal. My
| claim would be that for a wideclass of such interventions
| the very same genes will do radically different things,
| producing quite different kinds of animal.
|
| Likewise, after birth, different ecologies will make
| significant differences/etc.
| pfdietz wrote:
| Every aspect that makes humans human (or mice mice) was
| produced by evolution, and therefore must be based on
| genetics. That's because evolution only acts on
| information encoded in genes (no, epigenetic information
| doesn't count).
|
| Denying this is basically being a creationist.
| jltsiren wrote:
| There is a side channel for information: the human (or
| the mouse) itself. A genome is, among other things, a
| recipe for making X, assuming that you already have X.
| But if you don't have X and don't know what it looks
| like, it's not clear that the genome contains enough
| information to make X.
| ghhyfx wrote:
| Right, some information is encoded in the egg. You can't
| take human DNA and put it in a mice egg. And then you
| have the womb which itself directs growth in the first
| stages.
|
| DNA is the machine code, but you need a compatible
| computer to run it.
| concordDance wrote:
| > The human genome is only 20k genes, 90%+ we share with a
| mouse.
|
| Non-protein-coding genes are still genes.
|
| > Children are still taught there are such things as dominant
| traits, and genes for eye colour
|
| I'm 90% sure you've got some motte-and-bailey definitions
| going on here. Dominant traits as commonly defined are
| plentiful, e.g. various skin issues.
| PaulHoule wrote:
| Part of the molbio story in the last year or so is that
| people are getting some insight into the regulatory
| function of what they used to call "Junk DNA".
| dekhn wrote:
| There are definitely things like dominant and recessive
| traits- it's just that only a limited number of genes
| actually demonstrate this behavior in a non-ambiguous way.
|
| Eye color and hair color have been studies pretty intensively
| and they definitely have models which are more complex than
| "if you have value Y at position 37 of gene X, you have blue
| eyes". The way it's normally stated is that we can explain
| 50% of the heritance of eye color using a limited set of
| SNPs.
|
| What we don't have is a comprehensive model of how complex
| phenotypes arise from genotypes. This is only because of
| historical oversimplification, and partly because the
| underlying causality of phenotypes is remarkably
| sophisticated due to a combination of many factors,
| overlapped with enormous amounts of noise and confounding
| factors.
| oldgradstudent wrote:
| > Eye color and hair color have been studies pretty
| intensively and they definitely have models which are more
| complex than "if you have value Y at position 37 of gene X,
| you have blue eyes". The way it's normally stated is that
| we can explain 50% of the heritance of eye color using a
| limited set of SNPs.
|
| That's all very nice, but can you predict eye color from a
| genetic test with reasonable confidence?
|
| That a very simple question and the answer is apparently a
| resounding no.
| dekhn wrote:
| I think the answer is, "yes, we can predict eye color
| from a genetic test" but the prediction will be
| probabilistic and frequently wrong. For example:
| https://www.ancestry.com/c/traits-learning-hub/eye-color
| and the references suggest such a test exists.
| robwwilliams wrote:
| Definitely NOT a resounding no. Here are two recent
| studies that might be of interest.
|
| https://pubmed.ncbi.nlm.nih.gov/32488945/
|
| https://www.science.org/doi/10.1126/sciadv.abd1239
|
| The second study demonstrates that more than 50% of
| variance in eye pigmentation can be explained by simple
| additive effects.
|
| " We identify 124 independent associations arising from
| 61 discrete genomic regions, including 50 previously
| unidentified. We find evidence for genes involved in
| melanin pigmentation, but we also find associations with
| genes involved in iris morphology and structure. Further
| analyses in 1636 Asian participants from two populations
| suggest that iris pigmentation variation in Asians is
| genetically similar to Europeans, albeit with smaller
| effect sizes. Our findings collectively explain 53.2%
| (95% confidence interval, 45.4 to 61.0%) of eye color
| variation using common single-nucleotide polymorphisms."
|
| Hardly a resounding no.
| jjtheblunt wrote:
| > I would say this "golden age" is more a discovery of how
| everything we have previously believed is BS.
|
| Whoa. I think your wording works more accurately observing
| previous beliefs are only a subset of a bigger picture, and
| are at times context dependent in such bigger pictures.
| bpodgursky wrote:
| > Children are still taught there are such things as dominant
| traits, and genes for eye colour, etc. Yet we've no idea of
| the full genetics of eye colour.
|
| Adding FUD doesn't help. There are perfectly knowable things
| to teach kids --
|
| - Blue-eyed parents have blue-eyed kids.
|
| - Brown eyed parents have brown-eyed kids, if they are
| homozygous.
|
| - Sometimes, two brown-eyed parents have recessive alleles!
| But it's rare!
|
| - A blue-eyed parent and a brown eyed parent will have ~50%
| blue-eyed children
|
| You don't have to 100% characterize all hazel and green
| shades to capture most of the state of knowledge. These are
| 99.9% true. You're just trying to cast doubt on an
| increasingly well-understood field, akin to people trying to
| pick apart climate change research.
| robwwilliams wrote:
| I don't understand your arguments at all. Why does the
| homology of genes between apes and rodents bother you? They
| are part of a single "super-primate" clade--the
| euarchontoglires:
| https://en.wikipedia.org/wiki/Euarchontoglires
|
| This degree of overlap is entirely expected and accepted and
| has been for many decades before fully genome sequence gave
| us hard numbers.
|
| Can you clarify your second paragraph? Heritability is not a
| controversial topic but if you are saying the estimates are
| often abused, then I definitely will agree.
|
| There are clearly dominant traits (and recessive traits).
| Huntington's disease is the canonical example. If a student
| does not understand Mendelian genetics first they will not be
| able to understand complex quantitative genetics.
|
| Your last statement is extreme. Do you also think that all of
| Newtonian physics is BS and should not be taught to kids.
| photochemsyn wrote:
| The sheer amount of data being generated seems overwhelming.
| For example these researchers created a new family tree of just
| the grass species (very import agriculturally and industrially
| of course):
|
| > "The research team generated transcriptomes -- DNA sequences
| of all of the genes expressed by an organism -- for 342 grass
| species and whole-genome sequences for seven additional
| species."
|
| https://www.psu.edu/news/eberly-college-science/story/new-mo...
|
| This does allow analysis of very complex but desirable traits
| like drought tolerance, which involve a great many genes, but
| sorting through these huge volumes of data to ascertain which
| gene variants are the most important is challenging at best.
| robwwilliams wrote:
| True. and the quality of the genome assemblies is getting far
| better thanks to sequencing technologies that can easily
| generate data for 200,000 consecutive basepairs.
|
| But just to circle back on junk DNA---most of it is non-
| functional baggage---the result of our constant battles with
| viruses and replication errors.
| Cupertino95014 wrote:
| Honest, no-agenda question: if you go to East Africa where homo
| sapiens originated, there is (reportedly) much more genetic
| diversity than in the rest of the world. I haven't been there,
| myself.
|
| So forgetting scientific studies for the moment: if you just walk
| around in a city, is that apparent to you? Do you think, "Wow,
| there sure are a lot of different types of people here?"
| robwwilliams wrote:
| No you would not. The underlying level of genetic diversity is
| often not reflected in the diversity of classical phenotypes
| and traits.
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