Phylogenetic clunkiness

Writing a bacterial phylogenetics paper is probably the most agonizing type of paper to write due to the clunkiness of the language. But it's not the jargon that make life hell, it's the missing jargon that make it hard. The quantity of jargon actually make life a bit easier, but the lack of some blatantly useful words makes it painfully clunky and stuffy.

Reading a phylogenetics paper is generally visually painful due to the frequent usage of italics and "quote" marks. A phenomenon that I once read described aptly as a "typographic circus" by someone on a Wikipedia talk page. The italics are for taxa described validly according to the bacteriological code, whereas quotes are reserved for candidate taxa which have not been validated yet —the bugs exist, but nobody has done the paperwork. Nevertheless, the aesthetic problem is trivial compared to the lexal ones…

One such problem is the lack of trivial names (common names).
Only a few groups of  bacteria have trivial names and for some reason in microbiology, unlike botany, scientific names are rarely "trivialised", a process of making an English word for a member of a taxa, for example, a crustacean is a member of the family Crustacea and a bromeliad is a member of the genus Bromelia.
The most notable exceptions are a proteobacterium (a member of the phylum Protobacteria), an enterobacterium (a member of the family Enterobacteriales) and a pseudomonad (a member of the genus Pseudomonas). This is a shame as it circumvents the repetitive clunkiness and stuffiness. Taxonomic names, after all, are labels for the group, which can adopt a metaphorical usage to denote one of its members, primarily due to the quirkiness of the Latin name: for example, a group of sheep is a flock, but calling a single sheep a flock would sound awkward, whereas calling a sheep an Ovis sounds less weird, just technical. However, the phrase "a member of the" becomes really trite really quickly, one alternative is to use the word sp. (species), but it is still a bit weird: is the supposed to be the indefinite article "an" before Ovis sp.? A further perk is that a trivial name often allows adjectives to be formed, which is much nicer to read than a noun used adjectivally or "of the".
This last note is related to another problem with the Latin grammar of the nomenclature: all higher ranked names are plurals in Latin whereas there is only one of them (there are several members). In Latin (and other romance languages) collective nouns are plurals, whereas in English they are generally singulars (grammatical concord), but can be treated as plurals in informal speech (notional concord), e.g. the Alps is a mountain range (grammatical concord), the band are playing (notional concord). It does seem like a minor nuisance, but it gets really knotty when describing relationships and last common ancestors… on the plus side though the pride in the "look at my fancy Latin" is pretty nice.

Metabolic engineering Breaking Bad

Disclaimer: Obviously, this is a speculative what-if out of intellectual curiosity and by no means condones narcotics and their creation.
Update: This post was written when the hit show Breaking Bad was still on TV and the chemistry on the show were commonly discussed and joked about, so please keep that in mind.

The logo of Breaking Bad had it been bio.

Half the issues in Breaking Bad could have been solved if they had been using biocatalysis and metabolic engineering. The catch is that nobody has made a production strain and it is not a simple task.

Biocatalysis: greener and safer

Some time soon, biocatalysis and metabolic engineering will replace many heterocatalytic processes as it is more efficient, cheaper, safer and greener.
Worldwide, there is a big problem of exploding methamphetamine labs. This problem could be fixed by switching from toxic and dangerous heterocatalysis processes to green and safe biocatalysis ones.

Requirements

So if Walt and Jessie wanted to win the green chemistry award, what would they need to do?
Their major problem is the starting material and the production steps. So the whole lot. Therefore, they need to do metabolic engineering.
The major issue is that methamphetamine is not a natural compound, so extensive engineering would be needed to produce the final steps. However, once they laboriously made a production strain, they would need to set up a large-scale bioreaction, i.e. a brewing tank, extract the product by phase-separation, remove the solvent and purify by crystallisation as they normally do. Then the only worry then is that they may be as contaminant-prone as Hank is at brewing.

Starting point

Methamphetamine is a compound that looks like phenyalanine, but on the chiral α-carbon there is methyl group instead of a carboxyl one and the amine group is methylated.
The natural molecules most similar to methaphetamines are pseudoephedrine and ephedrine. These two diastereomers differ from the former in having a hydroxyl group (in different chiral orientations) on the carbon adjacent to the benzene ring. The biosynthetic pathway is known (PMID 22502775), but requires eleven steps, which have not been assembled exogenously in an orderly way.
Additionally, to convert ephedrine to methamphetamine new enzymes need to be engineered for the hydroxyl reduction, which is problematic. Consequently, ephedrine biosynthesis might not be the best route and instead something more radical may be in order.

Ephedrine biosynthesis

Ephedrine gets its name from the genus Ephedra, whose members produce it. Unfortunately the selective pressures for plant secondary metabolism are rather unusual (cool) and as a result the metabolic routes get a tad tortuous.
If one were to forget how plants like to do things, one would guess a simple pathway with a similar logic to threonine biosynthesis be present. Namely, the carboxyl is twice reduced and the remaining hydroxyl is isomerised to the right place.

The final step (not pictured), the N-methylation, would be simply accomplished by a SAM-dependent methyltransferase and is the only part that is correct.
In the isomeration step, one might anticipate that an enamine-ketimine tautomerism followed by an attack by water might occur ruining the effort. However, the isomerisation of homserine to threonine is done via a PLP enzyme which holds the amine, so this isn't the problem.

The problem is plants like to make second metabolism in an OCD way, starting from specific compounds (e.g. geranyl-PP, farnesyl-PP, cinnamoyl-CoA, coumaroyl-CoA, malonyl-CoA and acetyl-CoA), preferably using decarboxylative condensation.
The ephedrine pathway is no exception and shares the beginning of the pathway with many other compounds Phenylanine > cinnamic acid > cinnaomyl-CoA>>benzoyl-CoA. Then the unique part is that the benzoyl-CoA is condensed with pyruvate, reduced and transaminated.
In reality, whereas the full pathway is known, the genes themselves are not, simply because nobody has sequenced E. sinica. Although a group in 2009 has gone to the effort of making yeast take up the DNA of E. glauca via ion implantation —no kidding around there!— and make ephedrine, but they did not sequence a few hybrids or similar, but instead did a lot of tedious work with primers (PMID: 19280123). Consequently, their experiment would need to be repeated, but with sequencing.
Once the various genes are cloned into E. coli, preferable into a strain that overproduces phenylalanine (eg. from PMID: 17880710), the pathway would be optimised, giving an ephedrine-producing strain.

The last step

The last step is the trickiest.
After those few years of work are done, the hydroxyl needs to be removed reductively.
Hydroxyl/water is a terrible leaving group when not activated (i.e. phosphorylated) or using a resonance trick. Biochemically, hydroxyl groups are normally removed in two steps, the hydroxyl group is removed without adding an electron pair to the molecule by a hydroxylase which leaverages a nearby tautomerise-able group, therefore leaving a double-bonded carbon, which is then reduced by a reductase.  In some rare cases, the hydroxyl is reduced away directly. The most famous example is ribonucleotide reductase. The mechanism is rather satanic —a radical-assisted dehydration coupled to oxidation of the C3′ alcohol to a ketone, which starts with a HAT from the adjacent carbon (C3′), resulting in a carbonyl radical that provides a powerful electronic driving force for eliminating water at C2′ (pinacol rearrange with radical vibes), and ends in a proton-coupled electron transfer.
The dehydration route is a problematic option however. A modified 3-hydroxyacyl-ACP dehydrase and the enoyl-ACP reductase from the fatty acid biosynthetic pathway seem like good candidates. However, the dehydrated enolamine would spontaneously tautomerise and hydrolyse as mentioned above.
This might not be that catastrophic as the product would be phenylpropanone, which being similar to phenylpropane-dione, the product of the pyruvate-benzoyl-CoA condensation. It might be promiscuously transaminated again by the cathionine transaminase or by phenylamine transaminase.
Nevertheless it is an odd way of doing things.
The N-methylation must be done last as the product is slippery being so hydrophobic. Normally, biochemistry likes to put a handle to hold stuff like that, such as phosphates, CoA and glycosides. In this case, a N-glycosilation would be a good option. The best bet, however, would be to move the N-methylation step after the hydroxyl reduction, the methyltransferase cannot discern between the precursor for ephedrine or pseudoephedrine, so it is probably fairly accommodating towards amphetamine.

Crazy way

The carboxyl group needs to be replaced with a methyl group. This is not an option from a biochemists' perspective as C-C bonds cannot be made that easily, unless by condensation or transmethylation on aromatic structures. In a typical methyltransferase the methyl donor is SAM, while the acceptor is a nucleophile (Lewis base), such as an amine or a hydroxyl that has been deprotonated by a catalytic acid. From a technical point of view as far as I can tell there should not be anything forbidding a PLP and SAM dependent decarboxylative C-methylation. After a decarboxylation the negative charge is partially absorbed by the PLP (electron sink), leaving an nucleophilic secondary aldimine. The enzymatic reside that favoured the departure of the carboxyl group (say, catalytic lysine) might compete with the SAM though.

In the literature there is no sign of such a reaction: there is a decarboxylative O-methyltransferase (PMID: 22247507) and the various cases of SAM and PLP dependent enzymes, e.g. aminomutases, rely on SAM as a radical donor. There are some enzymes that point towards the possibility of such a C-methyltransferase, such as on an enol-ketone tautomerism (PMID: 5490210 and PMID: 17784761). Nevertheless, such an enzyme, if possible, would require a lot of work and luck to pull off. So the safer option might sound a lot longer, but has a higher chance of working...

Selection

A side question is how to select for better variants. To evolve a strain to make methamphetamine an way to select for one is obviously needed.
The traditional way would be to assay for those compounds by HPLC, but this would mean that the variants would be screened laboriously (especially in light of the optimisation required).
An option for a high-throughput approach is to make a transcription factor that responds only to the substance needed, so that it activates a fluorescent reporter which can be selected by a FACS (eg. PMID: 22276138). Unfortunately, the targets of amphetamines and those of catecholamines are membrane receptors. So the phenylalanine binding TF, tyrR-econded, would be a good candidate for engineering.

Toxicity

The oral murine LD50 of methamphetamine is slightly higher than capsaicin (55 vs. 46 mg/kg), so it is probably non-toxic to bacteria and due to its hydrophobicity it can be phase-separated easily from the aqueous environment. So a least one bit would be straight-forward.

Conclusion

Given the recombination and sequencing for gene identification, the many rounds of engineering and so forth, it would be five years if they are lucky. So metabolic engineering breaking bad would not start even at its fifth season...
And it would be expensive to do and there is no guarantee that their strain would remain safe — copying Walter's formula was an issue, here it would require only a stolen tube.
In brief, it would actually be a real pain to do and take years to cobble together, so unfortunately, metabolic engineering cannot make Walter and Jessie more green and free of precursor woes...

Life expectancy in Middle-Earth: elves and mortality tables

If Uruk hai drove buses the

war of the ring would have been short. 

A scary thought: I have an a priori chance of one in a thousand of dropping dead within next time this year (qx) in New Zealand, which is far more likely than winning the kiwi lotto (on a lotto day, 1:4M). Life is unfair, eh?

Luckily, I am not doing anything dangerous nor have any underlying conditions hence the a priori —although, I have not bought a lotto ticket either.

If I were in my nineties the chances change to a one in three or four per year, so the above figure is really low really. The reason is obvious, namely deterioration due to old age.

80% of the probability for young folk to die is due to external causes, which means accidents, homicide, suicide or war. For the elder folk it is due to diseases such as cancer. Boys do much more stupid stuff than girls, therefore for a woman of my age, the chances drop to one in three thousand.

The life expectancy is around 67 years in developed countries, but what would it be if one did not age?

Agerasia is the mythical state where one does not grow old. It is different from immortality as it does not include invulnerability: the probability of external causes still applies. As this probability does not change with age, age of death would follow a geometric distribution (and not a Gompertz–Makeham curve —thanks, Wikipedia!—) and the mean will consequently be 1/p. This means that on average a kiwi male would live 1,300 years, whereas a female 5,500 years.

In fantasy and science fiction, long-lived or agerasic humans and humanoids often appear, but those figures do not match the above…

In The Lord of the Rings, the dwarves had a life expectancy of 250 years or so the web informs me because they age slower than men. The elves do not grow old and lived about 1,000 years —Galadriel (Kate Blanchett) was probably one of the oldest and was a bit over 5,000 years. Middle Earth would just slightly more dangerous than New Zealand, but not by much. (In (ir)reality, elves are hardier than men, so the comparison is slightly unfair.) Possibly unsurprisingly, the US, on the other hand, is slightly more dangerous than Middle Earth.

In Iain M. Banks's Culture novels the folk of the Culture are said to live on average 400 years. The figure is so low because they get utterly bored after a while and kick the bucket, however one chap lived for 10,000 years, but he was rather bonkers.

In the bible, the patriarchs before the great flood lives for a long time. Their age of death are given which is really handy, but there are only ten of them and one, Enoch, did not technically die. Despite the small sample size, they lived on average 912 years, but the numbers are curious as they all died between 900 and 1,000 which is statistically impossible both under a geometric and a Gompertz distribution. The explanation that they get a "millenium crisis" at 900 does not fit as it is written they die of super-old age (which hits all of a sudden). Given that only Abel dies of external causes (1 in 10), it could be deduced that antediluvian Israel was much safer than New Zealand, Middle Earth or the US, but whatever rabbi wrote down the numbers wasn't well versed with statistics, so the bias is too strong for any conclusions.

Sources: Wikipedia, NZ life tables, some bible website, Iain Bank's Hydrogen Sonata and several unutterably nerdy LotR sites…

A map of Britain through a kaleidoscope

Captain Cook and chums may have gone where no white man had gone before, but, despite the romantic nobility of setting forth into the unknown, creativity in naming was not a job prerequisite.
This sentiment is perfectly told in a Mitchell and Webb sketch where a captain calls an bewilderingly new land in Australia after dreary southern Wales.
It does have curious upsides: I proudly told people from Portsmouth, New Hampshire in New England, that I came from Portsmouth, Hampshire in England, which amused me —it bemused them who had never realised the existence of a place without "New" slapped in front of it.
I am perpetually fascinated by the shuffled order that bares little resemblance to the original one. In New Zealand Windsor (in the South Island) is nowhere close to the river Thames (in the North Island), whereas Birkenhead (Liverpudlian suburb) is next to Devonport (Plymouthian suburb) in Auckland.
This raises the question whether on average towns and cities in an English-speaking new world country are geographically more spread out than their British namesakes.
After normalisation that is: the difference in size would bias this figure —after all the concept of "closeness" is seriously warped in new worlders.
On a gut instinct, I would used a simple arithmetic difference, so the final figure would be the number of British kilometers towns are more or less spread out on average, (as opposed to a ratio and geometric mean).
If new world towns were randomly distributed, the difference would not amount to much, but towns are not randomly distributed. The Aussie outback is truly empty and the Otago and Southland regions in New Zealand are one step short of being gàidhealtachd. My guess is that this figure would put British towns as more spread out than their newer namesakes if normalised.
Furthermore, many towns bear local names, such as the sublimely named Wooloomooloo, whereas other are missing: using least square regression the true namesakes of these missing towns could be found, although I have feeling the correspondence would be unidirectional.
However, getting the data for this inane quandary would be more hassle than it is worth, but it would be cool. One day…

Homologues and synonyms

All creatures great and small evolve, but evolution is not limited to the biological realm: languages evolve too and in a similar way.
My interest in languages stems from their ability to evolve with many similarities to enzyme evolution (and in light of not being able to spill the beans on my own research, I seem to post here a lot about words —And this is another!)
The technical words in linguistics differ from those in biology and I have yet to find an enlightening paper on the coevolution of synonyms and the parallels between language and genomes.

In enzymology, protein function and structure are not not always linked. Proteins with different functions can have similar structures having evolved from the same ancestral gene (functionally-divergent homologues) and proteins with different structures can perform the same function (functionally-convergent analogues).
In a language, words can have similar meanings, yet have different origins (synonyms) and words from the same origin can have different meanings.

New genes enter an organism via gene duplication, horizontal gene transfer or gene birth. Similarly, new words enter a language by duplication, loanwords (words of foreign origin) or onomatopoeiae.

English is a really great language for two reasons: it is my mother-tongue and it is a hybrid.
Regarding the latter reason, over a third of the words in the English dictionary were acquired from French due to the Norman invasion of 1066. The grammar and basic vocabulary remained that of Old English, whereas the advanced vocabulary was that of Old French.
A parallel to this can be drawn with the weird and wonderful bacterium Thermotoga maritima, 24% of whose genome is of archaeal origin: the replication and expression machinery is bacterial, but several metabolic routes are archaeal.

A loanword is a foreign word that is adopted in a language thanks to its real or percieved utility, whereas a horizontal gene transfer is an aquisition of a foreign gene in a genome thanks to its fitness benefits. The original spelling of loanwords are gradually lost in favour of a more compatible spelling and similarly the codon and amino acid compositions of trasferred genes also gradually change to match that of the new genome.

Often synomyms of different origins coexist, in English for a while the Old-Norse–originating window (vinauga, wind+eye), the Old-English–originating eagþyrl (eye+hole) and the Old-French–originating fenestre were coexisting, until one won. When French entered into the English language many synonyms died, but many survived in a figurative meaning, for example, enthrall litterally means to enslave, but nowadays it is used figurately, ie. capuring one's attention.
With genes the pressure to remove genes with identical function (be they paralogues, xenologues or analogues) depends on the selective pressure and in Eukaryotes they can coexist for some time.
Some words adopt alternative spellings, which can dissapear or gain different functions, such as the pairs yet and get, passed and past, and especial and special. Gene duplication does the same. In the IAD model of gene divergence, the new function comes before the amplification.

English, French and several other languages use the Latin alphabet to write words down. However, the phonetics of Latin lacks several sounds present in these and work-arounds are done. The letter h is used as a modified in English to make wh, th and ch sounds and vowel combinations allow extra vowel sounds. Old English used to be written with Anglo-saxon runes and then, with Christianity, switched over to the Latin one, bringing with it two heavily used runic letters absent in the Latin alphabet (þ and ƿ). However, as most typesetting letters were produced in France the letters died out. Despite the obvious simplicity they endow, new letters are very rarely added.
The work-around the lack of letters results in coding problems: the th group in Bath, Chatham Islands and Thailand differ, as the former is the fricative, the second is a word fusion (the H is not a modifier) and the latter is a plosive (a “violent” T). The only way to know is to know the exceptions or guess from the etymology, which can be misleading in thyme and Thames.
In protein several non-standard residues can be found. None of these use a recoded codon by itself, but require special sequences or post-transcriptional modifications, so the system differs slightly in that new letters (codons) cannot be added, but is similar in its workarounds.

Many differences exist, however.
Languages have grammar and generally authoritative bodies acting independantly of the evolution of the language (French academy).
Many suffices and prefices are highly constructive, a modularity that is hard to find in genes.
Enzymes have promiscuous function, minor non-physiological functions that can lead to new main activities: a property that is different in words. Words have multiple definitions and some are often confused. The word brothel used to mean prostitute, but it was confused with the word bordel and the meaning of the latter was bestowed on the former. Biannual traditionally means two-yearly, but its continual misuse as semestral means that the word has two discordant definitions, annulling its functionality. Genes have layers of regulation, whereas words don't. However, the metaphor could be stretch to equate grammar to regulation, but that may be wholly in the handwaving realm…