Byte Size Biology

Marketing yourself is a process you go through many times. The job hunt comes to mind — but not only. Academia is rife with self-marketing: grant applications, promotion & tenure reports, attracting students to your courses and to your lab,  competing for conference lecture slots, giving a lecture.

But not only academia, and not only in the present day.

Leonardo di ser Piero da Vinci was, among many other things, a civil and military engineer.  Marc Cenedella has this report on Da Vinci’s resume, sent to the Duke of Milan, who apparently was in need of some military hardware.  The resume, such as it is, is truly a great piece of self-marketing. Note how LDV tailors his resume to the Duke’s needs. He does not list his artistic achievements (which were many by the time), but only those achievements and skills that fit his prospective employer’s interests. My observations are in boldface.

“Most Illustrious Lord, Having now sufficiently considered the specimens of all those who proclaim themselves skilled contrivers of instruments of war, and that the invention and operation of the said instruments are nothing different from those in common use: I shall endeavor, without prejudice to any one else, to explain myself to your Excellency, showing your Lordship my secret, and then offering them to your best pleasure and approbation to work with effect at opportune moments on all those things which, in part, shall be briefly noted below.

1. I have a sort of extremely light and strong bridges, adapted to be most easily carried, and with them you may pursue, and at any time flee from the enemy; and others, secure and indestructible by fire and battle, easy and convenient to lift and place. Also methods of burning and destroying those of the enemy. [Before the legendary British WWII Bailey Bridge]

2. I know how, when a place is besieged, to take the water out of the trenches, and make endless variety of bridges, and covered ways and ladders, and other machines pertaining to such expeditions.

3. If, by reason of the height of the banks, or the strength of the place and its position, it is impossible, when besieging a place, to avail oneself of the plan of bombardment, I have methods for destroying every rock or other fortress, even if it were founded on a rock, etc.

4. Again, I have kinds of mortars; most convenient and easy to carry; and with these I can fling small stones almost resembling a storm; and with the smoke of these cause great terror to the enemy, to his great detriment and confusion. [Battlefield smoke].

5. And if the fight should be at sea I have kinds of many machines most efficient for offense and defense; and vessels which will resist the attack of the largest guns and powder and fumes.

6. I have means by secret and tortuous mines and ways, made without noise, to reach a designated spot, even if it were needed to pass under a trench or a river.

7. I will make covered chariots, safe and unattackable, which, entering among the enemy with their artillery, there is no body of men so great but they would break them. And behind these, infantry could follow quite unhurt and without any hindrance. [Yes, LDV invented the tank! Note also the combined infantry / armor tactics].

8. In case of need I will make big guns, mortars, and light ordnance of fine and useful forms, out of the common type. [Not only can I do it, I can do it cheaply, by re-purposing your existing ordinance.]

9. Where the operation of bombardment might fail, I would contrive catapults, mangonels, trabocchi, and other machines of marvelous efficacy and not in common use. And in short, according to the variety of cases, I can contrive various and endless means of offense and defense.

10. In times of peace I believe I can give perfect satisfaction and to the equal of any other in architecture and the composition of buildings public and private; and in guiding water from one place to another. [Dear Duke: you want to hire me even if you are not fighting, or you will want to keep me after your wars are over.]

11. I can carry out sculpture in marble, bronze, or clay, and also I can do in painting whatever may be done, as well as any other, be he who he may. [Another peacetime skill.]

Again, the bronze horse may be taken in hand, which is to be to the immortal glory and eternal honor of the prince your father of happy memory, and of the illustrious house of Sforza. [Catering to the employer's vanity. Gotta know how to do it right...]

And if any of the above-named things seem to anyone to be impossible or not feasible, I am most ready to make the experiment in your park, or in whatever place may please your Excellency – to whom I comment myself with the utmost humility, etc.” [I realize make big claims, but I can back them up. Just get me an interview.]

edw513 at Ycombinator.com has adapted this resume to fit current market needs:

If it worked for Leonardo da Vinci, maybe it could work for me. The next time I’m looking for a job, I’ll try this:“Most Illustrious Proprietor, Having now sufficiently considered the specimens of all those who proclaim themselves skilled developers of applications of business, and that the invention and operation of the said programs are nothing different from those in common use: I shall endeavor, without prejudice to any one else, to explain myself to your Company, showing your Management my secret, and then offering them to your best pleasure and approbation to work with effect at opportune moments on all those things which, in part, shall be briefly noted below.

1. I have a sort of extremely light and strong functions and modules, adapted to be most easily ftp’d, and with them you may pursue, and at any time combine them with others, secure and indestructible by standard mean time to failure of hardware and denial of service, easy and convenient to compile and catalog. Also methods of unzipping and storing the data of the customers.

2. I know how, when a website is besieged, to shard data onto the cloud, and make endless variety of mirrors, and fault tolerant disks and RAIDs, and other machines pertaining to such concerns.

3. If, by reason of the volume of the data, or the structure of the btrees and its indexes, it is impossible, when conducting a search, to avail oneself of sub-second response time, I have methods for benchmarking every process or other function, even if it were interpreted, etc.

4. Again, I have kinds of functions; most convenient and easy to ftp; and with these I can spawn lots of data almost resembling a torrent; and with the download of these cause great terror to the competitor, to his great detriment and confusion.

5. And if the processing should be on the desktop I have apps of many machines most efficient for data entry and reporting; and utilities which will satisfy the needs of the most demanding customers and users and consumers.

6. I have means by secret and tortuous scripts and modules, made without leaving tracks, to generate source code, even if it were needed to run on a client or a server.

7. I will make secure firewalls, safe and unattackable, which, entering among the hackers with their utilities, there is no body of crackers so great but they would break them. And behind these, software could run quite unhurt and without any hindrance.

8. In case of need I will make big properties, methods, and collections and useful forms, out of the common type.

9. Where the operation of compiling might fail, I would contrive scripts, functions, routines, and other parameter driven processes of marvellous efficacy and not in common use. And in short, according to the variety of cases, I can contrive various and endless means of data entry, reporting, and storage.

10. In times of low revenue I believe I can give perfect satisfaction and to the equal of any other in maintenance and the refactoring of code public and private; and in guiding data from one warehouse to another.

11. I can carry out code in Javascript, PHP, or C, and also I can do in network administration whatever may be done, as well as any other, be he who he may.

Again, the intranet app may be taken in hand, which is to be to the immortal glory and eternal honor of all your customers of happy memory, and of the illustrious house of Google.

And if any of the above-named things seem to anyone to be impossible or not feasible, I am most ready to make the experiment in your data center, or in whatever place may please your Businessperson – to whom I comment myself with the utmost humility, etc.”

Boys and girls, it can be done. Published in the Journal of Irreproducible Results (Where else?)

A nice take on the vi / emacs wars

Also, real programmers browse the web using the vimperator.

Speaking of sampling bacteria, this ties in well with the previous post about GEBA. And by “well” I mean “in an alternate-universe/ altered-consciousness manner”.

The voices in the song are sampled from this KFC employee training tape. The video won a prize in machinima.com. So if you like World of Warcraft, bacteria, KFC, sampled music, or any combination of the above, you’re gonna love this.

Floated in my email inbox recently. Bears blogging.

Dear Editor,

I would like to thank the editorial board and the referees for their comments and contributions to our manuscript. We have carefully considered the comments when rewriting the manuscript, and believe it to be much improved now…

…Oh, screw this. Let’s cut the bull. Mmkay?

Referee #1 did not even bother to read the paper. He basically glanced at the references, realized he was not cited enough to his taste, got pissed off, and attached a Pubmed dump of his papers in the last 10 years. All three of them. There is a reason none of these papers went beyond a single digit number of citations: they suck! Also, I fail to see how a paper discussing semantic distances as applied to an “endoplasmatic reticulum membrane elasticity ontology” has anything to do with my paper. Or with anything of interest, for that matter.

Referee #2 requested reanalysis of our data, using Boyle-Scott statistics. Applying Boyle-Scott statistics to our work would be like draping a hornet’s nest with clingwrap while wearing a bathing suit: a long and painful process which is utterly pointless. B-S statistics are exactly what they are, and if you think I will be bothered to do that, with my grad student finally graduating and taking off, you’re as delusional as Dr. Boyle was when he was researching REM sleep in cannabis-treated amphibians just before he went completely schizo and had to be locked up.

Referee #3 Actually read the manuscript carefully. Which is both commendable and rare. Unfortunately, judging by the comments presented, it was not my manuscript.

Finally, I would request that you as an editor grow a brain. Did you even read their comments before passing them on to me? Shipping out papers to referees, then getting them back, pasting them together and slapping on some boilerplate text from your journal’s editor’s site is not editorial work. In fact, a middle school student that volunteers in my lab wrote up a script yesterday that does just that. We are thinking of installing it in your esteemed journal’s author’s website and waiting to see if this editorial version of the Turing test would pass. We are very optimistic about the results, and we plan to write a paper about them.

Sincerely,

Prof. I. M. Irritated

I was recently reminded of this classic by Geoffrey James. Here are a few of my favorites. The whole text is available online.

In the beginning was the Tao. The Tao gave birth to Space and Time. Therefore Space and Time are Yin and Yang of programming.

Programmers that do not comprehend the Tao are always running out of time and space for their programs. Programmers that comprehend the Tao always have enough time and space to accomplish their goals.

How could it be otherwise?

Thus spake the master programmer:

“After three days without programming, life becomes meaningless.”

A novice asked the master: “I have a program that sometime runs and sometimes aborts. I have followed the rules of programming, yet I am totally baffled. What is the reason for this?”

The master replied: “You are confused because you do not understand Tao. Only a fool expects rational behavior from his fellow humans. Why do you expect it from a machine that humans have constructed? Computers simulate determinism; only Tao is perfect.

“The rules of programming are transitory; only Tao is eternal. Therefore you must contemplate Tao before you receive enlightenment.”

“But how will I know when I have received enlightenment?” asked the novice.

“Your program will then run correctly,” replied the master.

A novice asked the Master: “Here is a programmer that never designs, documents or tests his programs. Yet all who know him consider him one of the best programmers in the world. Why is this?”

The Master replies: “That programmer has mastered the Tao. He has gone beyond the need for design; he does not become angry when the system crashes, but accepts the universe without concern. He has gone beyond the need for documentation; he no longer cares if anyone else sees his code. He has gone beyond the need for testing; each of his programs are perfect within themselves, serene and elegant, their purpose self-evident. Truly, he has entered the mystery of Tao.”

I didn’t write this one, but I wish I did. I found it on Science after Sunclipse. I guess that a CC license can be safely applied to anonymous chain letters.

Today CBSG continues with its pointers for budding scientists with the second part on serving as a peer reviewer for papers and grants.

Okay, you’ve decided that you are going to reject a manuscript. The naive reviewer might think that it is enough to simply state the reasons for the rejection as clearly and succinctly as possible. But this overlooks a major issue: ensuring that the authors do not know that it is you who rejected the manuscript.

Because the peer review process is anonymous, this may seem like no concern, as long as you extirpate all references to your own work to keep your identity secret. Wrong! You have to keep in mind that no matter how crappy the paper is, the authors are going to be pissed that it is rejected, and they are going to immediately begin wracking their brains to identify referees who might have done the dirty on them. Most will form a list of at least 5 or 6 people that they think are likely to have screwed them. Since most papers are reviewed by no more than 2-3 reviewers, this means you have a good chance of being on the list even if you were NOT the reviewer. Thus, particular pains must be taken to direct the authors ire elsewhere. Several different means to accomplish this are described below:

1. Pretend that you are British. (Note — this does not work well if you actually are British).

Just a few decades ago, it was enough to include a liberal sprinkling of “rathers” and “doubtlesses” throughout the review, and convert all colors to colours, analyze to analyse, polymerize to polymerise, etc. However, the increasing intellectual and cultural cross-pollination brought by the internet has rendered such limited measures ineffective. Thus, you need to be au courant with all the most specific idioms available to the average Brit.

For example, you might want to refer to a poorly run gel as being “dodgy”, “gammy” or “a bit pear-shaped”. Especially effective are slang terms derived from cricket. This is because no self-respecting American knows anything about this sport (indeed, outside the British Commonwealth, cricket is universally reviled as the one sport even more boring than baseball). Here are some cricket-based phrases worked into sentences that you might include in a review. Instead of writing “Some of the data presented by the authors are mutually contradictory” write “The authors seem to have gotten themselves into a bit of a sticky wicket”.

Instead of writing “The documentation of morpholino efficacy by monitoring expression of exogenously provided target rather than the endogenous target is not quite fair” write “Using GFP-ponticulin as a read out for the morpholino effects is not quite cricket”. And, instead of writing “I was chagrined to see that the authors ignored the previous studies by the Jones lab”, write “the failure of the authors to cite the seminal studies of Jones and colleagues hit me for six”.

1B. Pretend that you are an American pretending to be British (Note: this does work if you are British, but does not work if you are American.) The strategy here is similar to #1 above, but instead of being a little bit subtle, you go straight over the top. Thus, instead of writing “I seriously doubt that anyone will believe …”: “Blimey! Blokes would have to be right daft if they were to believe …”

2. Pretend that you are Canadian. This is harder because the only major language difference between Americans and Canadians is that the latter tend to mispronounce words with the short O sound such that they rhyme with newt. Needless to say, this sort of thing is not manifest in written reviews.

However, the canny reviewer can draw on the one or two features of Canadian culture that are unique. Interestingly (in light of the cricket discussion above) most of these revolve around Canadian football. For example, you might allude to a paper not being ready for the Grey Cup yet (a reference to the Canadian equivalent of the Super Bowl), describe an experimental situation as being “3rd and long” (an allusion to the fact that there are only three downs in Canadian football) or argue that the authors need to “bring in a couple more coaches” (referring to the fact that Canadian football teams have 4 head coaches). Cite obscure Canadian journals: “J Can. Med. Assoc.” or “Can. J. Cardio.” No one outside of Canada reads these journals.

3. Pretend that you are German. This is even harder, because even if you know some German, you have to write your review in English for most journals. Be extremely precise and technical. You could also try simply putting the verb at the end of your sentences (as in “The experiments in figures 5 and 6 should repeated be”), however this runs the risk of having yourself labeled not as a German, but as an imbecile or an incarnation of Yoda. Alternatively cite organic chemistry articles from the late 19th and early 20th century that have never been translated into English. Cite German aricles during the 30s and 40s when the rest of Academia was trying its best to ignore German science.

3B. Pretend that you are an American pretending to be German; sprinkle the text with flavorful comments such as “Ach mein lieber!” or “Du spinnst!” Or, if a line of reasoning is particularly awful, “Ist gibt ein Blutbat en der Hoelle!” Stick umlauts on random words, and make liberal use of the eszett. Downside: the editor will conclude you have flipped.

4. Pick one of the people from you own list of 5-6 enemies and pretend to be that person. Heavily cite their work. Reference their obscure conference presentations. Arrogantly suggest that person’s methods in favor of the methods used in the paper, especially where they are clearly inapplicable

Respected Sir,

I am Distinguished Professor First Class Nebulous Nimbus, Department of Organismal Motility of the University Technicality of Upper Freedonia. I have many articles accepted and pending in PLoS Biology, PNAS, and BMC. Unfortunately I cannot pay the Open Access publication costs as my University has suffered abysmally from ill-advised investments in derivatives both partial and directional applied by the Math & Freakonomics department. A plaque on both their houses.

Sir, your reputation as a reverent and eminent scientist proceeds you. I have carefully sifted you for to assist Freedonian science from bottomless finance pit. I would be graciously to add  you  as honorific author in good position and standing to my articles, if you would be so kind as to send me Western Union the publication money needed by these journals in most urgent immediacy.

Please contact me in highest importunate on this matter: nebnim@ufd.ac.fd

Sincerely,

Docent Professor Doktor Nebulous Nimbus

(Celebrate #oaw09 Open Access Week)

A bit late in the day, but here are the Ig Nobel prize winners for 2009. Cut and pasted from Wikipedia. The prizes were awarded Thursday, Oct. 1, 2009 at
Sanders Theater, Harvard University, Cambridge, Massachusetts

2009

• Veterinary medicine: Catherine Douglas and Peter Rowlinson of Newcastle University, UK, for showing that cows with names give more milk than cows that are nameless.
• Peace: Stephan Bolliger, Steffen Ross, Lars Oesterhelweg, Michael Thali and Beat Kneubuehl of the University of Bern, Switzerland, for determining whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle.
• Biology: Fumiaki Taguchi, Song Guofu and Zhang Guanglei of Kitasato University Graduate School of Medical Sciences in Sagamihara, Japan, for demonstrating that kitchen refuse can be reduced more than 90% in mass by using bacteria extracted from the feces of giant pandas.
• Medicine: Donald L. Unger of Thousand Oaks, California, US, for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand but not his right hand every day for more than 60 years.
• Economics: The directors, executives, and auditors of four Icelandic banks — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa (and for demonstrating that similar things can be done to an entire national economy).
• Physics: Katherine K. Whitcome of the University of Cincinnati, Daniel E Lieberman of Harvard University and Liza J. Shapiro of the University of Texas, all in the US, for analytically determining why pregnant women do not tip over.
• Chemistry: Javier Morales, Miguel Apatiga and Victor M. Castano of Universidad Nacional Autonoma in Mexico, for creating diamond film from tequila.
• Literature: Ireland’s police service for writing and presenting more than 50 traffic tickets to the most frequent driving offender in the country – Prawo Jazdy – whose name in Polish means “Driving Licence”.
• Public Health: Elena N. Bodnar, Raphael C. Lee, and Sandra Marijan of Chicago, US, for inventing a bra that can be quickly converted into a pair of gas masks – one for the wearer and one to be given to a needy bystander.
• Mathematics: Gideon Gono, governor of Zimbabwe’s Reserve Bank, for giving people a simple, everyday way to cope with a wide range of numbers by having his bank print notes with denominations ranging from one cent to one hundred trillion dollars.

Stephen Colbert had an interesting lineup for the past two nights: Richard Dawkins on Sep 30, and Francis Collins last night. Enjoy the vids:

The Colbert Report	Mon – Thurs 11:30pm / 10:30c
Richard Dawkins
www.colbertnation.com
Colbert Report Full Episodes Political Humor Michael Moore

The Colbert Report	Mon – Thurs 11:30pm / 10:30c
Francis Collins
www.colbertnation.com
Colbert Report Full Episodes Political Humor Michael Moore

Somehow, sharing the same problems with Uri Alon makes me feel almost absolved of the sins against my own family in spending Sundays at the lab. Almost:

---

Ron Laskey has a whole collection of songs, published as an audiobook in Cold Spring Harbor Laboratory Press. (I guess CSHL Press does not qualify as an indie record label). Unfortunately, not available as mp3s, not legally, at least.

He is known for coining the term chaperone, a class of proteins that prevent other proteins from aggregating and help them fold to the correct shape. He actually has a song about that, where he apologizes for giving to the scientific world a term infamous for its Victorian prudishness. Here is another song, on how students and teachers replace the brain-dead atmosphere of the classroom for the equally brain-dead atmosphere of the conference:

5. Question: “You know, our group has been working on this for a long time, and we found that…”

Really means: “How come you got invited to talk about this and not I?”

4. Question:  “Have you tried using Y instead of X?”

Really means: “We are doing the same thing using Y, since we can’t afford to use X on our budget. But we haven’t had results in the past two years, and you totally scooped us. Is there any way we can actually get results using Y?”

3. Question: “So where do you think this work is going?”

Really means: “I was just scratching my head, and the microphone runner thought I was raising my hand and handed me the mike.  Now that I actually have the mike, I might as well ask something”.

2. Question:  “You know, I was just talking about this recently with Bigshot1 and Bigshot2, and they said that…”

Really means:  “Hey, look at me!  I’m important enough to have engaged both Bigshot1 and Bigshot2 together in a conference. (They couldn’t get away because it was the conference dinner with free booze).”

1. Question:  “It seems that this whole field of…. is filled with very exciting prospects. We have been looking into…. and Bigshot3 has recently published in Science….(3-4 minutes more in the same vein)  so my question is: what are your thoughts?”

Really means: “Muahahaha. By hijacking Q&A time, I got to present at this conference even though I was not invited to. Sucks to the Program Committee”

Warning: frivolously geeky and technical  post, which can be best defined as “science methodology esoterica”, and from which you can learn absolutely nothing useful.  If you don’t get what’s going on, then it’s probably for the best, because this is a complete waste of time.

Specific Aim 1:  find the longest word in English composed of the Protein 20-letter alphabet.

Method: I like gawk for quick & dirty text processing:

gawk 'BEGIN {daword="a"} \
/[BbJjOoUuXx]/ {next} \
length($1) > length(daword) {daword=$1} \
END  {print daword}' /usr/share/dict/web2

acetylphenylhydrazine

OK, this kinda sucks. I want a real word in English, not a chemical portmanteau. Let’s see what a top 10 list looks like:

gawk 'BEGIN {for(i=1;i<=10;i++) daword[i]="a"} \
/[BbJjOoUuXx]/ {next} \
{for (i in daword) {if (length($1) > length(daword[i])) {daword[i]=$1;break}}} \
END  {for (i=1;i<=10;i++) print length(daword[i]), daword[i]}' \
/usr/share/dict/web2 | sort -nr

And the result:

21 pentamethylenediamine
21 acetylphenylhydrazine
20 paraphenylenediamine
20 metaphenylenediamine
20 interparenthetically
19 transcendentalistic
19 semiantiministerial
19 platymesaticephalic
19 peripachymeningitis

19 misapprehensiveness

Interparenthetically. How lovely if you do your bioinformatics in Lisp.

Specific Aim 2: Lets BLAST this

Method: NCBI TBLASTN:

>
emb|CAK04910.1|  novel protein similar to vertebrate Hermansky-Pudlak syndrome
3 (HPS3) [Danio rerio]
Length=1041

 GENE ID: 563666 LOC563666 | similar to LOC398456 protein [Danio rerio]

 Score = 30.3 bits (64),  Expect =    22
 Identities = 9/10 (90%), Positives = 10/10 (100%), Gaps = 0/10 (0%)

Query  2    NTERPARENT  11
            NTERPAR+NT
Sbjct  505  NTERPARKNT  514

>
ref|XP_664219.1|  hypothetical protein AN6615.2 [Aspergillus nidulans FGSC A4]
 sp|Q5AYL5.1|SEC16_EMENI  RecName: Full=COPII coat assembly protein sec16; AltName: Full=Protein
transport protein sec16
 gb|EAA58144.1|  hypothetical protein AN6615.2 [Aspergillus nidulans FGSC A4]
Length=1947

 GENE ID: 2870538 AN6615.2 | hypothetical protein [Aspergillus nidulans FGSC A4]
(10 or fewer PubMed links)

 Score = 30.3 bits (64),  Expect =    22
 Identities = 10/13 (76%), Positives = 10/13 (76%), Gaps = 0/13 (0%)

Query  1   INTERPARENTHE  13
           INTE PARE T E
Sbjct  61  INTESPAREETAE  73

>
ref|XP_001707965.1|  hypothetical protein [Giardia lamblia ATCC 50803]
 gb|EDO80291.1|  Hypothetical protein GL50803_14341 [Giardia lamblia ATCC 50803]
Length=247

 GENE ID: 5700874 GL50803_14341 | hypothetical protein
[Giardia lamblia ATCC 50803] (10 or fewer PubMed links)

 Score = 30.3 bits (64),  Expect =    22
 Identities = 9/12 (75%), Positives = 10/12 (83%), Gaps = 0/12 (0%)

Query  4    ERPARENTHETI  15
            ER ARE THE+I
Sbjct  221  EREAREKTHESI  232

>
ref|YP_002191813.1|  conserved hypothetical protein [Streptomyces clavuligerus ATCC
27064]
 gb|EDY50943.1|  conserved hypothetical protein [Streptomyces clavuligerus ATCC
27064]
Length=565

 GENE ID: 6836469 SSCG_04068 | hypothetical protein
[Streptomyces clavuligerus ATCC 27064]

 Score = 29.5 bits (62),  Expect =    39
 Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 1/20 (5%)

Query  1    INTERPARENTHETICALLY  20
            I  ERP R +T E I ALLY
Sbjct  219  ITAERPQRTDT-EAIGALLY  237

Interesting, but the e-values are insignificant. PSI-BLAST, BLASTP against metagenomic sequences in CAMERA all came up with zip.

Conclusion: I totally wasted my time doing this, and yours reading this. Therefore, I need more funding to check the other words on the list.