White Beard
Active member
...now I’m going to have to learn enough about Single Nucleotide Polymorphism to have an opinion on whether it’s a scam or not.
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Phylos Galaxy - Landrace discussion
- Thread starter Thule
- Start date
...now I’m going to have to learn enough about Single Nucleotide Polymorphism to have an opinion on whether it’s a scam or not.
White Beard
Active member
Thanks, that was very useful...haven’t digested it all yet.
Based on that (and a few more), what Phylos has done is much less scary or whatever: it has raw data about the existence and location of alleles within the cannabis samples they have. That’s all. None of this is sequenced, as near as I can tell, these are site comparisons for variant protein structures. It could tell us how many cannabis plants (out of how many total) have blue eyes, or freckles, or pistil color - IF we knew which allele (SNP instance) was the allele for blue-eyed cannabis....
Too little is known to make this data valuable except to research, and it would/will be *expensive* research to conduct, and we are talking YEARS, even with supercomputers. This data is essentially useless until an actual cannabis genome is completed, at which point, what Phylos has will be just one more chunk of data: it will only matter in context of the whole, and it almost certainly won’t be special.
Until then, they can’t even extrapolate from their data. What there trying to sell won’t be worth anything for a long time...I think that underscores the idea that this is a double-headed con, and not at all the stealing of DNA as we’ve been thinking about it.
yes, that's it, and the reason I don't believe in this whole phylos conspiracy. (except SNP's don't have to be the cause of an allele themselves, a lot of SNP's are just variations in the dna without effect, but if they're located within a gene or closely linked to it, you can still use the SNP as a marker for that allele)
linking the SNP's to traits to use in breeding may be a bit easier as you imagine it though, IF you've got live plants.
the way you'd start out using markers for breeding would be to make a map of such snp's, so that you get a map-skeleton with 1 marker every 5 cM (centimorgan, a unit for measuring distance in dna that's based on recombination frequency, instead of actual physical distance).
then next step you grow out a population that varies on these SNP's, and you write down all kinds of traits they express, and then use a bunch of statstics etc to link those expressed traits to the markers you found earlier. this is called phenotyping.
so phylos could do stuff up to that phenotyping step, but since they don't have live plants, they can't link any markers to traits that way(however they could do the phenotyping on their own plants, and maybe that way identify some markers that could be used on their galaxy-data too, however you can't just translate a marker from one small population to every plant in existence, especially if the marker is not in the gene itself but just closely linked)
speaking about sequencing the cannabis genome, there are already cannabis genomes available online. I accidently sequenced some cannabis dna once for a class, the BLAST-search showed similarity with stored cannabis genomes, so that's how I knew the primer amplified the wrong dna.
I'm not sure how good and complete those data are, but they're there, available online for free.
linking the SNP's to traits to use in breeding may be a bit easier as you imagine it though, IF you've got live plants.
the way you'd start out using markers for breeding would be to make a map of such snp's, so that you get a map-skeleton with 1 marker every 5 cM (centimorgan, a unit for measuring distance in dna that's based on recombination frequency, instead of actual physical distance).
then next step you grow out a population that varies on these SNP's, and you write down all kinds of traits they express, and then use a bunch of statstics etc to link those expressed traits to the markers you found earlier. this is called phenotyping.
so phylos could do stuff up to that phenotyping step, but since they don't have live plants, they can't link any markers to traits that way(however they could do the phenotyping on their own plants, and maybe that way identify some markers that could be used on their galaxy-data too, however you can't just translate a marker from one small population to every plant in existence, especially if the marker is not in the gene itself but just closely linked)
speaking about sequencing the cannabis genome, there are already cannabis genomes available online. I accidently sequenced some cannabis dna once for a class, the BLAST-search showed similarity with stored cannabis genomes, so that's how I knew the primer amplified the wrong dna.
I'm not sure how good and complete those data are, but they're there, available online for free.
White Beard
Active member
That all sounds good, but there are several black boxes in there, and those things are *notoriously* hard to predict in terms of making them and working with them intelligently.
My readings said that SNPs occur in non-coding sections as well as coding sections...and that SNPs in coding sections *are* alleles - that’s what they *do* in coding sections, is give expression to phenotypic variance
I think it’s helpful to remember that we’re basically reverse-engineering an extraordinarily complex alien tech we barely understand....
My readings said that SNPs occur in non-coding sections as well as coding sections...and that SNPs in coding sections *are* alleles - that’s what they *do* in coding sections, is give expression to phenotypic variance
I think it’s helpful to remember that we’re basically reverse-engineering an extraordinarily complex alien tech we barely understand....
well, you're on the right track, but I think you're missing a few nuances.
an allele is a variant of a whole gene. a SNP is just one basepair in the DNA that's different(single nucleotide). a SNP could result in an allele, but even if it results in an allele, it's not the same(although in that case, it's kind of a semantic kind of issue, not a big deal on a forum like this but important to get all the details of what you're saying come across right if you're talking to a scientist). but that's just a minority of all SNP's.
as you correctly said, it matters wether that one changed nucleotide is within the coding part or non-coding part. so there you have option 1 where a SNP is not resulting in an allele. there are many non-coding parts, also within genes you have parts that get cut out before it's translated into a protein(exon/intron).
but even an SNP within the coding part doesn't have to mean anything for the protein that's produced, so no different allele.
DNA into proteins works with sets of 3. each amino acid in the protein is coded by a specific combination of 3 nucleotides. however, the same amino-acid can be coded by different 3 nucleotide-codes. so if just 1 of those 3 changes, it might still code for the exact same amino-acid. for example, did a quick google and found this picture listing nucleotide combinations and the amino acid it codes for:
so most of the time, mutations of a single nucleotide have no effect at all.
however, it can have a much more drastic effect if the reading frame is changed. for example if you have an indel(insertion or deletion) of a single nucleotide somewhere, all combinations of 3 after that point shift one nucleotide to the right or left, possibly coding for different amino acids.
an allele is a variant of a whole gene. a SNP is just one basepair in the DNA that's different(single nucleotide). a SNP could result in an allele, but even if it results in an allele, it's not the same(although in that case, it's kind of a semantic kind of issue, not a big deal on a forum like this but important to get all the details of what you're saying come across right if you're talking to a scientist). but that's just a minority of all SNP's.
as you correctly said, it matters wether that one changed nucleotide is within the coding part or non-coding part. so there you have option 1 where a SNP is not resulting in an allele. there are many non-coding parts, also within genes you have parts that get cut out before it's translated into a protein(exon/intron).
but even an SNP within the coding part doesn't have to mean anything for the protein that's produced, so no different allele.
DNA into proteins works with sets of 3. each amino acid in the protein is coded by a specific combination of 3 nucleotides. however, the same amino-acid can be coded by different 3 nucleotide-codes. so if just 1 of those 3 changes, it might still code for the exact same amino-acid. for example, did a quick google and found this picture listing nucleotide combinations and the amino acid it codes for:
so most of the time, mutations of a single nucleotide have no effect at all.
however, it can have a much more drastic effect if the reading frame is changed. for example if you have an indel(insertion or deletion) of a single nucleotide somewhere, all combinations of 3 after that point shift one nucleotide to the right or left, possibly coding for different amino acids.
Hi
As far as I know Phylos is using SNP's in order to stablish relationships among strains. You can make a cladogram or a phylogenetic tree with that info. Also you can use any other genetic marker to stablish phylogenetic relationships, or even aminoacid protein sequences.
https://en.wikipedia.org/wiki/Genetic_marker
https://en.wikipedia.org/wiki/Phylogenetics
I have been warned several times, and I read here and there, this and that, about if Phylos is collecting seeds with some dark purpouses, as patenting all strains, creating GMO marijuana or inserting DNA from dead seeds into yeasts in order to get specific cannabinoids + terpenes profiles. Or even they plan to make their own seedbank. I think that is all too conspiranoic or paranoid. But you are free to believe what you want.
Of course it is a company and they work for money. But I wouldn't feel too much worried about what they are going to do with all those old dead seeds they get.
Are all of you going to create your own seedbank, or your marijuana company or dispensary and you are worried about if you cannot sell your seeds later because they would have been pantented? I really think it is too paranoid. If you don't want anybody steal your work with your genetics, simply keep them only for you. Or let the seeds die in a hot drawer for decades, or much better in an airtight ziplock bag inside the fridge or frozen. Nobody will make money with your seeds that way.
What I can really blame Phylos are two things.
The first one is the terrible decission choosing modern polyhybrids as outgroups. In all serious cladograms and phylogenetic trees you use as outgroup a basal related species or strain.
https://en.wikipedia.org/wiki/Outgroup_(cladistics)
The second one is that strange galaxy in 3D full of shinny bright colored dots. It is very flashy and striking and very funny to watch when you are high. But along the outgroups it is a big mess.
A simple cladogram or a phylogenetic tree would have been more useful and accurate. However less flashy and entertaining to navigate when you are high or baked
https://en.wikipedia.org/wiki/Cladogram
As far as I know Phylos is using SNP's in order to stablish relationships among strains. You can make a cladogram or a phylogenetic tree with that info. Also you can use any other genetic marker to stablish phylogenetic relationships, or even aminoacid protein sequences.
https://en.wikipedia.org/wiki/Genetic_marker
https://en.wikipedia.org/wiki/Phylogenetics
I have been warned several times, and I read here and there, this and that, about if Phylos is collecting seeds with some dark purpouses, as patenting all strains, creating GMO marijuana or inserting DNA from dead seeds into yeasts in order to get specific cannabinoids + terpenes profiles. Or even they plan to make their own seedbank. I think that is all too conspiranoic or paranoid. But you are free to believe what you want.
Of course it is a company and they work for money. But I wouldn't feel too much worried about what they are going to do with all those old dead seeds they get.
Are all of you going to create your own seedbank, or your marijuana company or dispensary and you are worried about if you cannot sell your seeds later because they would have been pantented? I really think it is too paranoid. If you don't want anybody steal your work with your genetics, simply keep them only for you. Or let the seeds die in a hot drawer for decades, or much better in an airtight ziplock bag inside the fridge or frozen. Nobody will make money with your seeds that way.
What I can really blame Phylos are two things.
The first one is the terrible decission choosing modern polyhybrids as outgroups. In all serious cladograms and phylogenetic trees you use as outgroup a basal related species or strain.
https://en.wikipedia.org/wiki/Outgroup_(cladistics)
The second one is that strange galaxy in 3D full of shinny bright colored dots. It is very flashy and striking and very funny to watch when you are high. But along the outgroups it is a big mess.
A simple cladogram or a phylogenetic tree would have been more useful and accurate. However less flashy and entertaining to navigate when you are high or baked
https://en.wikipedia.org/wiki/Cladogram
Hi
As far as I know Phylos is using SNP's in order to stablish relationships among strains. You can make a cladogram or a phylogenetic tree with that info. Also you can use any other genetic marker to stablish phylogenetic relationships, or even aminoacid protein sequences.
https://en.wikipedia.org/wiki/Genetic_marker
https://en.wikipedia.org/wiki/Phylogenetics
I have been warned several times, and I read here and there, this and that, about if Phylos is collecting seeds with some dark purpouses, as patenting all strains, creating GMO marijuana or inserting DNA from dead seeds into yeasts in order to get specific cannabinoids + terpenes profiles. Or even they plan to make their own seedbank. I think that is all too conspiranoic or paranoid. But you are free to believe what you want.
Of course it is a company and they work for money. But I wouldn't feel too much worried about what they are going to do with all those old dead seeds they get.
Are all of you going to create your own seedbank, or your marijuana company or dispensary and you are worried about if you cannot sell your seeds later because they would have been pantented? I really think it is too paranoid. If you don't want anybody steal your work with your genetics, simply keep them only for you. Or let the seeds die in a hot drawer for decades, or much better in an airtight ziplock bag inside the fridge or frozen. Nobody will make money with your seeds that way.
What I can really blame Phylos are two things.
The first one is the terrible decission choosing modern polyhybrids as outgroups. In all serious cladograms and phylogenetic trees you use as outgroup a basal related species or strain.
https://en.wikipedia.org/wiki/Outgroup_(cladistics)
The second one is that strange galaxy in 3D full of shinny bright colored dots. It is very flashy and striking and very funny to watch when you are high. But along the outgroups it is a big mess.
A simple cladogram or a phylogenetic tree would have been more useful and accurate. However less flashy and entertaining to navigate when you are high or baked
https://en.wikipedia.org/wiki/Cladogram
View Image
That Cladogram looks very usefull and can be easy to understand
this kind of genetic tree...
mine thoughts was anyway that Phylos is a work of some nutjob
and was use Seed...Finder as there you can understand something
and what genetics are in cross..
Thanx for share,am agree with you 100%..
White Beard
Active member
Hi
As far as I know Phylos is using SNP's in order to stablish relationships among strains. You can make a cladogram or a phylogenetic tree with that info. Also you can use any other genetic marker to stablish phylogenetic relationships, or even aminoacid protein sequences.
https://en.wikipedia.org/wiki/Genetic_marker
https://en.wikipedia.org/wiki/Phylogenetics
I have been warned several times, and I read here and there, this and that, about if Phylos is collecting seeds with some dark purpouses, as patenting all strains, creating GMO marijuana or inserting DNA from dead seeds into yeasts in order to get specific cannabinoids + terpenes profiles. Or even they plan to make their own seedbank. I think that is all too conspiranoic or paranoid. But you are free to believe what you want.
Of course it is a company and they work for money. But I wouldn't feel too much worried about what they are going to do with all those old dead seeds they get.
Are all of you going to create your own seedbank, or your marijuana company or dispensary and you are worried about if you cannot sell your seeds later because they would have been pantented? I really think it is too paranoid. If you don't want anybody steal your work with your genetics, simply keep them only for you. Or let the seeds die in a hot drawer for decades, or much better in an airtight ziplock bag inside the fridge or frozen. Nobody will make money with your seeds that way.
What I can really blame Phylos are two things.
The first one is the terrible decission choosing modern polyhybrids as outgroups. In all serious cladograms and phylogenetic trees you use as outgroup a basal related species or strain.
https://en.wikipedia.org/wiki/Outgroup_(cladistics)
The second one is that strange galaxy in 3D full of shinny bright colored dots. It is very flashy and striking and very funny to watch when you are high. But along the outgroups it is a big mess.
A simple cladogram or a phylogenetic tree would have been more useful and accurate. However less flashy and entertaining to navigate when you are high or baked
https://en.wikipedia.org/wiki/Cladogram
View Image
Nahhh,,, I'd love a tree like this,,, it's silly how it is atm,, imo
CannaZen
Well-known member
Yeah without oldschool/heirlooms as the basal, how do we know the difference of relativity, we have poly-hybrids its difficult for me to ascertain valuable information from phylos's database. So they have orbits and i have to visually look at distance in a galaxy... it would be better measured in descent line if at all possible, cannot they make genetic correlations? cannot they correlate cannabinoid alleles, growth structure alleles with descent lines etc. Without a point of origin we do not know where we are going. They do not have me as a customer, i consider that a loss.
apparently the enzymatic process of yeast were modified to produce cannabinoids from sugar.
https://www.sciencedaily.com/releases/2019/02/190227131838.htm
apparently the enzymatic process of yeast were modified to produce cannabinoids from sugar.
https://www.sciencedaily.com/releases/2019/02/190227131838.htm
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CannaZen
Well-known member
Yeast isnt Cannabis, sir. I would not be concerned about cannabinoids being gmo.. the only concern for that matter is environmental implications and i would not consider it escaping into the wild a natural threat. of concern about where i procure resin i suppose i do not expect to be the main producer i much rather prefer to cultivate my own, if i can. Its about growing self-dependent from others and sharing the surplus. Its really a benign plant. Your worried they wont share their rose plants with everyone for free use and i agree, I think they can own their genetic augmentation but they do not own the entirety of the genome of natural organisms as a whole they must respect every gene of every chromosome as intended for open use. Its a philosophical argument.
Edit: i'd like to add that they are modified organisms yes but when your basing genes sourced from natural organisms domesticated or not, you cant claim ownership of the function of the genome as a whole only, the mutation or modification perhaps, yes, but certainly not the entire reversion of genes aka organism, like say their collection of genetic modification makes up 10% of the collective function of the genome as a whole and they patent the entire organism or something, they really dont own the entire genome. I suppose they're saying its an entirely unique organism but we both know if the genes came from natural open-use sources those genes should remain for open use. I'm just speculating here.
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White Beard
Active member
Let me be the first to say that breeding itself is a form of genetic modification ...the ugh I know that’s not what you meant...but here’s my harebrained thought-bomb for the night:
It’s crossed my mind more than once, when I consider plants such as cannabis, such as ginseng, tanguai, astragalus, gan cao...I am *stunned* frequently by how well-tuned they are to our metabolism, the depth and breadth of effect they have on our fundamental systems, how many intimate aspects of our basic functionality are enhanced, streamlined, tweaked, regulated, even enabled by them...more than once, I say, it has crossed my mind that they are almost TOO perfect to be natural, unmodified plants...as if, they’d been *made* for us or by us, or engineered by a civilization far more knowledgeable than ours.
These are some of the oldest plants in human use, and they ALL have multiple chemical pathways to improve the wearing of a meat suit year after year.... in many ways I think cannabis is the prize of the bunch in terms of bounty. Was this accomplished by villagers working largely in isolation sporadically is widely separated parts of the planet, without Mendel or Burbank to help them? With virtually no exchange of information?
Yep, stoned again...
It’s crossed my mind more than once, when I consider plants such as cannabis, such as ginseng, tanguai, astragalus, gan cao...I am *stunned* frequently by how well-tuned they are to our metabolism, the depth and breadth of effect they have on our fundamental systems, how many intimate aspects of our basic functionality are enhanced, streamlined, tweaked, regulated, even enabled by them...more than once, I say, it has crossed my mind that they are almost TOO perfect to be natural, unmodified plants...as if, they’d been *made* for us or by us, or engineered by a civilization far more knowledgeable than ours.
These are some of the oldest plants in human use, and they ALL have multiple chemical pathways to improve the wearing of a meat suit year after year.... in many ways I think cannabis is the prize of the bunch in terms of bounty. Was this accomplished by villagers working largely in isolation sporadically is widely separated parts of the planet, without Mendel or Burbank to help them? With virtually no exchange of information?
Yep, stoned again...
Sexual reproduction or even mutations in clones introduce variability in the DNA.
But usually it is said GMO as lab genetic modification (usually trangenics) no common breeding done since thousand years ago.
https://en.wikipedia.org/wiki/Genetically_modified_food#History
It is not the same the transition from teozintle to corn, than the Round-Up ready GMO.
But usually it is said GMO as lab genetic modification (usually trangenics) no common breeding done since thousand years ago.
https://en.wikipedia.org/wiki/Genetically_modified_food#History
It is not the same the transition from teozintle to corn, than the Round-Up ready GMO.
For the record are you saying you are Pro GMO cannabinoids?
To me GMO Cannabinoids is the same as GMO cannabis.
As I tried to say in the other post:
The text books may not agree but a rose by any other name is still a rose is it not?
What you get is not gmo cannabis, but gnb cannabis.
gnb - genetic new breeding.
gnb - genetic new breeding.
W
Water-
the texts books dont agree with you beacuse you are wrong.
use your brain instead of your ego
I may be wrong but to me GMO cannabinoids is the same as GMO cannabis.
What do we want from cannabis?
Cannabinoids right?
Take away the cannabinoids and what is left?
Waste material, like after extraction.
Well if the cannabinoids are from a GMO source then how are they not GMO Cannabinoids?
So how would you label it?
Non-Cannabis GMO canabinoids??
Can you really extract Cannabinoids from a GMO product and not label them GMO?
Can you then sell it as a natural product?
If so then this may be worse than GMO cannabis itself.
What do we want from cannabis?
Cannabinoids right?
Take away the cannabinoids and what is left?
Waste material, like after extraction.
Well if the cannabinoids are from a GMO source then how are they not GMO Cannabinoids?
So how would you label it?
Non-Cannabis GMO canabinoids??
Can you really extract Cannabinoids from a GMO product and not label them GMO?
Can you then sell it as a natural product?
If so then this may be worse than GMO cannabis itself.
CannaZen
Well-known member
[FONT=Arial, Helvetica, sans-serif]n[/FONT]
Except that they're cannabinoids you just dont like the point of origin. accept it, i will go no further on this matter.
