What-If 0153: "Peptides" [removed]

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ps.02
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What-If 0153: "Peptides" [removed]

Postby ps.02 » Mon Dec 05, 2016 6:53 pm UTC

Lysine-Isoleucine-Arginine-Alanine wrote:What is the longest English word you can spell using the one letter abbreviations of the 20 genetic amino acids? What about the three letter abbreviations? What would the resultant peptides look like?

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There may not be a lot of real English words to be made from those TLAs (Randall did miss hisser), but I see a rich vein of second-order sniglets. ("Words that should be in the list of sniglets, but aren't.") E.g., phegly, promet, proalacys, thrasp, argile, leuser, gluser.

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Re: What-If 0153: "Peptides"

Postby jozwa » Mon Dec 05, 2016 6:56 pm UTC

"Mostly Armless" would be a PERFECT name for a Haunter in Pokemon Go if it weren't slightly too long.


What a strange thing to say when Pokemon Sun and Moon are out.

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Re: What-If 0153: "Peptides"

Postby speising » Mon Dec 05, 2016 7:07 pm UTC

"What-is" 0153

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Re: What-If 0153: "Peptides"

Postby pebkac » Mon Dec 05, 2016 8:53 pm UTC

If you find a peptide containing a longer word, you could be eligible for a Nobel Prize


Would that be the Nobel Prize for Physiology or Literature?

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Re: What-If 0153: "Peptides"

Postby Soupspoon » Mon Dec 05, 2016 9:03 pm UTC

With rare but extant Selenocysteine (O) and Pyrrolysine (U) and without the colonial spelling, "Deinsitutionalisation" is a perfectly cromulant peptide chain... Or is that a Pyrrolysine-Valene-Glutamic Acid-Arginine-Isoleucine-Asparagine-Threonine-Glutamic Acid-Arginine-Leucine-Glutamic Acid-Cysteine-Threonine-Selenoceistine-Alanine-Leucine-Isoleucine-Serine-Alanine-Threonine-Isoleucine-Pyrrolysine-Aspargine?

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Flumble
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Re: What-If 0153: "Peptides"

Postby Flumble » Mon Dec 05, 2016 11:25 pm UTC

Did Randall purposefully interpret "what about the three-letter abbreviations" as "the three-letter sequences" rather than "the letters used in the three-letter abbreviations"?
He did interpret "using the one-letter abbreviations" as "any multiplicity of the set of letters that occur in the abbreviations" rather than "pick letters from the list" or "make words with exactly all the aminoacids occuring once".

In any case you can't spell Flumble, so I'll have to develop a virus which encodes for tRNA variations that accept new aminoacids and which hacks into the genome to produce a FLUMBLE sequence after every stop codon. Including the codon(s) in the virus of course.


For posterity: Kimiko hacking into the human genome.

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Durandal_1707
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Re: What-If 0153: "Peptides"

Postby Durandal_1707 » Tue Dec 06, 2016 5:16 am UTC

Hey, I caught a typo! "Deinstitutionalization," not "deinsitutionalization." As written, it would only have been 21 letters, not 22.

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Re: What-If 0153: "Peptides"

Postby CharlieP » Tue Dec 06, 2016 8:42 am UTC

I thought it was a different question for a second. I can get GAGA and TACT.
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Re: What-If 0153: "Peptides"

Postby HES » Tue Dec 06, 2016 9:52 am UTC

If there are only 20 genetic amino acids, and they have distinct one-letter abbreviations, why bother having three-letter abbreviations?
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Flumble
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Re: What-If 0153: "Peptides"

Postby Flumble » Tue Dec 06, 2016 10:25 am UTC

HES wrote:If there are only 20 genetic amino acids, and they have distinct one-letter abbreviations, why bother having three-letter abbreviations?

The three-letter ones use letters that correspond to the name of the amino acid. Now one could say that's not terribly helpful because the names of the amino acids are also made-up nonsense (unless you know the etymology), but it seems like people in the field like to remember names rather than single letters.

Or maybe the three-letter abbreviations are designed for forward compatibility. Researchers are incorporating other amino acids in synthetic biology, so maybe we'll see aditions to the proteinogenic list in the future. :D

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Re: What-If 0153: "Peptides"

Postby KarenRei » Tue Dec 06, 2016 12:59 pm UTC

This question is really weak. Is knowledge of grep and the mere existence of "/usr/share/words" really that rare of a skillset?

egrep -i "^[ARNDCEQGHILKMFPSTWYV]*$" /usr/share/dict/words | awk '{print length, $0}' | sort -n | cut -d " " -f2-

egrep -i "^(ALA|ARG|ASN|ASP|CYS|GLU|GLN|GLY|HIS|ILE|LEV|LYS|MET|PHE|PRO|SER|THR|TRP|TYR|VAL)*$" /usr/share/dict/words | awk '{print length, $0}' | sort -n | cut -d " " -f2-

I recommend tailing them.

Examples (and numbers of Google hits):

characteristically (6,6m hits) (best 18-letter)
...
dimethyltryptamine (349k hits)
...
disenfranchisement (1,1m hits)
...
hypersensitivities (152k hits)
...
interparliamentary (313k hits)
...
parliamentarianism (225k hits)
...
representativeness (2m hits)
...
transcendentalists (485k hits)
...
interdepartmentally (55k hits) (best 19-letter)
...
anticapitalistically (14k hits)
antiecclesiastically (2700 hits)
antimilitaristically (5730 hits)
antiparliamentarians (5750 hits)
characteristicalness (1910 hits)
dimethylanthranilate (1700 hits)
hypergrammaticalness (5490 hits)
hypersensitivenesses (2950 hits)
interdifferentiating (3290 hits)
interparenthetically (6630 hits)
Llanfairpwllgwyngyll (390k hits) (best 20-letter)
metaphenylenediamine (38k hits)
paraphenylenediamine (97k hits) (best 21-letter)
phenylaceticaldehyde (1690 hits)
representativenesses (2750 hits)
semicapitalistically (2270 hits)
antimaterialistically (5240 hits)
hyperaggressivenesses (994 hits)
pentamethylenediamine (35k hits) (best 22-letter)
selectivitysenescence (2160 hits)
preinferredpreinferring (727 hits) (best 23-letter)

And...

Lev
lys
Lys
met
MET
pro
PRO
ser
SER
trp
tyr
Tyr
val
Val
argala (member of the stork family, Basque revolutionary; 239k hits)
Argile (french for clay, so exists in place names and the like; 12,1m hits)
hisser (one who hisses, techno band from Finland, etc; 2,1m hits)
proser (writer of prose; 721k hits, though mostly typos like "word proser")
serval (wild African cat; 6,4m hits)
valval (coconut vegetable curry; 256k hits)
Last edited by KarenRei on Wed Dec 07, 2016 4:11 pm UTC, edited 4 times in total.

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Re: What-If 0153: "Peptides"

Postby FOARP » Tue Dec 06, 2016 1:35 pm UTC

In 1995, researchers isolated several proteins produced during these infections, looking for possible targets for antibodies. One of the proteins they found was WYSLNGKIRAVDVPK, or GKIRAV for short.

...The bad news is that the researchers filed a patent which includes this sequence. The patent, published in 1999, gives the researchers exclusive control over this protein. If Kira wants to mess around with the protein, she could—in theory—be sued.

The good news is that in 2013, the Supreme Court struck down this type of gene patent. The case, Association for Molecular Pathology v. Myriad Genetics, Inc., involved the patents protecting tests for genetic cancer risk. That means Kira is totally free to produce as much WYSLNGKIRAVDVPK as she wants.


Wrong on so many levels.

Firstly, the patent was filed, based on a PCT filed in the UK, in many other countries than the US, with the first document in the patent family being published in 1995. We aren't told where Kira comes from so it isn't clear that the US patent would be the one relevant to her research, or even that she comes from a place in which a patent has been granted.

Secondly, the US, like many other jurisdictions, has a research exemption that allows research to be carried out on the patented subject matter for certain purposes. This exception is narrow in the US (my understanding is it only covers research for the purpose of getting approvals) but in other countries it is broader.

Thirdly, whilst some of the independent claims are directed to a purified bacterial protein expressed during infection due to streptococci, and this at least appears to be a compound found in nature of the type found unelligible in Myriad, it is not entirely clear that all of the claims (particularly claim 10) are of this nature. Not being a biologist it is hard for me to say, but a claim to recombinant DNA (which I understand is made in the lab) would seem not to fall within this exception unless that DNA is already found in nature.

Fourthly, any and all of the above is moot because the patent should have already expired.

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The Snide Sniper
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Re: What-If 0153: "Peptides"

Postby The Snide Sniper » Tue Dec 06, 2016 4:44 pm UTC

Did this What If? just get unpublished?
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Shadowman615
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Re: What-If 0153: "Peptides"

Postby Shadowman615 » Tue Dec 06, 2016 4:56 pm UTC

The Snide Sniper wrote:Did this What If? just get unpublished?


Hmmm. I saw it for a second about an hour ago -- meant to come back and read -- and now it's missing.

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Re: What-If 0153: "Peptides"

Postby Soupspoon » Tue Dec 06, 2016 5:30 pm UTC

Durandal_1707 wrote:Hey, I caught a typo! "Deinstitutionalization," not "deinsitutionalization." As written, it would only have been 21 letters, not 22.

Ahhh.. I saw that it wasn't based upon "institute", but: a) didn't count the letters, and b) didn't for one moment think that making it "...institut.." rather than "...insitut.." (the latter something I'd considered rooted upon the same root as "situational") would have made it one better... Fail on my part.

But does this open up even longer words*? I don't know. Maybe you'd have to ask a counterantidisensituationalisationistish person for their point of view..?

* Using UK spelling, and allowing the 21st/22nd O and U peptides, as noted, of course.

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Re: What-If 0153: "Peptides"

Postby HES » Tue Dec 06, 2016 5:55 pm UTC

The Snide Sniper wrote:Did this What If? just get unpublished?

What-If 153 wrote:
Whoops
This article is still in progress. An early draft was unintentionally posted here thanks to Randall's troubled approach to git, and it took a little bit to get everything sorted out and rolled back. Sorry for the mixup!
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Re: What-If 0153: "Peptides"

Postby The Snide Sniper » Tue Dec 06, 2016 7:03 pm UTC

HES wrote:
The Snide Sniper wrote:Did this What If? just get unpublished?

What-If 153 wrote:
Whoops
This article is still in progress. An early draft was unintentionally posted here thanks to Randall's troubled approach to git, and it took a little bit to get everything sorted out and rolled back. Sorry for the mixup!

That's a shame. Well, I hope to see the finished article.
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KarenRei
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Re: What-If 0153: "Peptides"

Postby KarenRei » Wed Dec 07, 2016 12:09 pm UTC

Soupspoon wrote:With rare but extant Selenocysteine (O) and Pyrrolysine (U) and without the colonial spelling, "Deinsitutionalisation" is a perfectly cromulant peptide chain...


Well, geez, if you're going to do that then you can do "pneumonoultramicroscopicsilicovolcanoconiosis" (45 letters) ;) Or if you want a word that wasn't originally coined to be a long word, "dichlorodiphenyltrichloroethane" (31 letters). Or if you want ones that aren't chemicals, "electroencephalographically" and "microspectrophotometrically" (27 letters)

If we apply that to the other challenge (adding in SEC and UAG).... hmm, it actually doesn't add anything longer to the list, or even a new six-letter word. We could get up to nine letters if someone would invent amino acids with the following TLAs:

AMPhisile
DISproval
hisSINgly
MetACOmet
metaspERM
PREserval
proCESser
proLARval
PrometHEA
propheTIC
propheTRY
proproFIT
prosecTED
prosecTOR
prosecUTE
proSINgly
prothrIFT
proTOMala
proVINgly
serRATile
serREFile
servalINE

Ed: here's three more that require just one new TLA, but use it twice:

aspERSERS
thrINGING
TINTINgly

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Re: What-If 0153: "Peptides"

Postby kugo2006 » Sun Dec 11, 2016 4:25 am UTC

so like.... did this what-if disappear?

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Re: What-If 0153: "Peptides"

Postby ConMan » Sun Dec 11, 2016 10:24 pm UTC

kugo2006 wrote:so like.... did this what-if disappear?
The Snide Sniper wrote:
HES wrote:
The Snide Sniper wrote:Did this What If? just get unpublished?

What-If 153 wrote:
Whoops
This article is still in progress. An early draft was unintentionally posted here thanks to Randall's troubled approach to git, and it took a little bit to get everything sorted out and rolled back. Sorry for the mixup!

That's a shame. Well, I hope to see the finished article.
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Re: What-If 0153: "Peptides"

Postby FOARP » Tue Jan 03, 2017 3:40 pm UTC

kugo2006 wrote:so like.... did this what-if disappear?


Yeah, and since it happened right after my post pointing out the patent law issues with it I'm going to imagine that it was my fault.

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Re: What-If 0153: "Peptides"

Postby Randall » Wed Feb 08, 2017 2:29 am UTC

There's an archive of the original here

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Re: What-If 0153: "Peptides"

Postby SDK » Tue Feb 14, 2017 9:43 pm UTC

Thanks, Randall.
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