Proteomics on a Mac

Thank whichever gods you do or don't believe in, it is finally possible to do all your proteomics data processing on a Mac. And I'm not even talking about Windows and Boot Camp. Mac processing power/memory and virtual machine technology have finally caught up to the point where you can run a Windows VM for all your Trans-Proteomic Pipeline/Xcalibur/Windows-only-whathaveyou programs in one window and get at your data storage and presentation options on your Mac side without any problems.

I am praising the skies for this as of right now as I figure it out. Given the last five years of ridiculously ponderous switching back and forth between machines, I feel like someone who just found out there are THESE ROUND THINGS that you can attach to your BOX and scoot it along so much faster than dragging it!

Steps for EZ-proteomics:

1. Get a new Macbook Pro with all the extra trimmings

2. Install VMWare Fusion, create a Windows Virtual Machine

3. Install all your data analysis software on the virtual machine side, have fun dragging data files back and forth right in the window!

4. CHACHING! Profit with your new lightning-fast productivity!

(thanks to my postdoc colleague "K" and proteomics IT specialist "L" for opening my eyes to this smooth new world)

Yay books meme, thanks drda! (lol and juniorprof) Some of these I know I have read even though I can't remember much about them... I read a LOT but to be honest, most of it is science fiction. I really have read the entire bible, although I skimmed a lot of the deuteronomy booooring stuff.

Bold = read
italics = started but not finished
plain = totally unread

1 Pride and Prejudice - Jane Austen

2 The Lord of the Rings - JRR Tolkien
3 Jane Eyre - Charlotte Bronte
4 Harry Potter series - JK Rowling
5 To Kill a Mockingbird - Harper Lee
6 The bible
7 Wuthering Heights - Emily Bronte
8 Nineteen Eighty Four - George Orwell

9 His Dark Materials - Philip Pullman
10 Great Expectations - Charles Dickens
11 Little Women - Louisa M Alcott

12 Tess of the D’Urbervilles - Thomas Hardy
13 Catch 22 - Joseph Heller
14 Complete Works of Shakespeare
15 Rebecca - Daphne Du Maurier
16 The Hobbit - JRR Tolkien
17 Birdsong - Sebastian Faulks
18 Catcher in the Rye - JD Salinger
19 The Time Traveller’s Wife - Audrey Niffenegger
20 Middlemarch - George Eliot
21 Gone With The Wind - Margaret Mitchell
22 The Great Gatsby - F Scott Fitzgerald

23 Bleak House - Charles Dickens
24 War and Peace - Leo Tolstoy
25 The Hitch Hiker’s Guide to the Galaxy - Douglas Adams
26 Brideshead Revisited - Evelyn Waugh
27 Crime and Punishment - Fyodor Dostoyevsky
28 Grapes of Wrath - John Steinbeck

29 Alice in Wonderland - Lewis Carroll
30 The Wind in the Willows - Kenneth Grahame
31 Anna Karenina - Leo Tolstoy
32 David Copperfield - Charles Dickens
33 Chronicles of Narnia - CS Lewis

34 Emma - Jane Austen
35 Persuasion - Jane Austen
36 The Lion, The Witch and The Wardrobe - CS Lewis

37 The Kite Runner - Khaled Hosseini
38 Captain Corelli’s Mandolin - Louis De Bernieres
39 Memoirs of a Geisha - Arthur Golden
40 Winnie the Pooh - AA Milne
41 Animal Farm - George Orwell
42 The Da Vinci Code - Dan Brown
43 One Hundred Years of Solitude - Gabriel Garcia Marquez

44 A Prayer for Owen Meany - John Irving
45 The Woman in White - Wilkie Collins
46 Anne of Green Gables - LM Montgomery
47 Far From The Madding Crowd - Thomas Hardy
48 The Handmaid’s Tale - Margaret Atwood
49 Lord of the Flies - William Golding
50 Atonement - Ian McEwan
51 Life of Pi - Yann Martel
52 Dune - Frank Herbert
53 Cold Comfort Farm - Stella Gibbons
54 Sense and Sensibility - Jane Austen
55 A Suitable Boy - Vikram Seth
56 The Shadow of the Wind - Carlos Ruiz Zafon
57 A Tale Of Two Cities - Charles Dickens
58 Brave New World - Aldous Huxley

59 The Curious Incident of the Dog in the Night-time - Mark Haddon
60 Love In The Time Of Cholera - Gabriel Garcia Marquez
61 Of Mice and Men - John Steinbeck
62 Lolita - Vladimir Nabokov
63 The Secret History - Donna Tartt
64 The Lovely Bones - Alice Sebold
65 Count of Monte Cristo - Alexandre Dumas
66 On The Road - Jack Kerouac
67 Jude the Obscure - Thomas Hardy
68 Bridget Jones’s Diary - Helen Fielding
69 Midnight’s Children - Salman Rushdie
70 Moby Dick - Herman Melville
71 Oliver Twist - Charles Dickens
72 Dracula - Bram Stoker
73 The Secret Garden - Frances Hodgson Burnett
74 Notes From A Small Island - Bill Bryson
75 Ulysses - James Joyce
76 The Bell Jar - Sylvia Plath
77 Swallows and Amazons - Arthur Ransome
78 Germinal - Emile Zola
79 Vanity Fair - William Makepeace Thackeray
80 Possession - AS Byatt
81 A Christmas Carol - Charles Dickens
82 Cloud Atlas - David Mitchell
83 The Color Purple - Alice Walker
84 The Remains of the Day - Kazuo Ishiguro
85 Madame Bovary - Gustave Flaubert
86 A Fine Balance - Rohinton Mistry
87 Charlotte’s Web - EB White
88 The Five People You Meet In Heaven - Mitch Albom
89 Adventures of Sherlock Holmes - Sir Arthur Conan Doyle
90 The Faraway Tree Collection
91 Heart of Darkness - Joseph Conrad
92 The Little Prince - Antoine De Saint-Exupery
93 The Wasp Factory - Iain Banks
94 Watership Down - Richard Adams
95 A Confederacy of Dunces - John Kennedy Toole
96 A Town Like Alice - Nevil Shute
97 The Three Musketeers - Alexandre Dumas
98 Hamlet - William Shakespeare- This isn’t in the ‘Complete Works’ @ #14?
99 Charlie and the Chocolate Factory - Roald Dahl
100 Les Miserables - Victor Hugo

oooh teh internets and meme


Lamest of my music, not in order (although, always a matter of perspective):

1. Green Day Bluegrass

2. The Moog Cookbook

3. Britney Spears' Greatest Hits

4. My own Garage Band songs

5. The Fifth Dimension

6. A crapton of MC Frontalot

I actually don't think ANY of it is lame, but it's the most likely for other people to think so.

It's the final countdown

nee nerr neeeeee nerrrrr, nee nerr nee neee nerrrrrr

Only 9 days left in the lab. Even though I don't actually move until the 12th of August. The rest of the days until that time are filled with making one more logistical visit to the new lab, various necessary weekend travels, and the 3-day proteomics course I am helping run and teach during my last week here.

I am cutting myself off from experiments after next week by bringing all my frozen stuff down with me to the logistical visit. That way I can't run any more gels, start any last "quick" cell experiments, try to do any more pulldowns, check any "last one thing." EXCEPT for the cells I'll still have growing, and the microscopy time I reserved for my LAST DAY ON THE OLD CAMPUS (damn that thing gets filled up so far in advance, otherwise I would have done it this week). And the last few peptides I want to make for the collaborator here before I leave...

But if I start any more experiments after this week, I'll just end up throwing them away without finishing the analyses and what is the point of that? I managed to get enough stuff figured out for my methodology in this last push to be as productive as humanly possible while I still had the whole setup in place. I now HAVE AN ASSAY even though a lot of little parameters need to be worked out, I know that my central technology development is going to work. I'm ready to be able to interpret other people's hands on the technique, rather than feeling like "Uhhh, well, who knows? I dunno if it even works so I can't tell if you just f'ed it up or not..."

You gotta leave yourself that last week. If I didn't have to spend three days immersing myself in this course (as well as all the prep I still need to do for the talks I am giving and the segments I am teaching, oh lordy), then I would have taken a nice vacation. Damn being addicted to this life.

Why pop is bad for you

My college biochemistry teacher used the different metabolic fates of fructose and glucose as an example when we were learning about that kind of thing, and it stuck with me that thusly, high fructose corn syrup in pop (I’m from Minnesota, that’s what it’s called) and juice is probably what makes little kids develop messed up metabolisms and have chronic energy/weight consequences for most people in the western world. Granted, the health effects of HFCS can’t be much different than those for sucrose (table sugar) used as a sweetener, since sucrose is 50:50 fructose/glucose and HFCS is only about 55:45 (depending on the formulation). But there are a lot of companies out there for whom the safety of cheap sweeteners like HFCS and sucrose are a big deal—as many others have noted before (e.g. in Fast Food Nation among other less pop-culturish writings), these fructose-rich sweeteners are in pretty much every kind of mass-produced food you can find at the grocery store: Pop, juice, crackers, BREAD, pasta sauces, every kind of snack cake/bar/cookie, frozen ready meals

Given the standard American and British diet, my crude estimate is that most people (particularly lower income people who can’t afford expensive fresh foods and probably don’t have a Whole Foods near their neighborhood anyway) get up to 50% of their daily calories from pop, juice and bread/convenience foods/snacks. That’s getting to be a pretty high percentage of fructose-rich calories EVERY DAY. Fructose (in contrast to glucose, which does not do this) is known to decrease circulating insulin and leptin (1) (which are important to telling the central nervous system that you ate, and so energy should be used rather than stored) and mess up the response levels of ghrelin, GLP-1(intact) and GIP—other important hormones for how the body recognizes the fact it has taken in nutrients and needs to do something with them. These things are thought to be parts of the mechanism by which fructose contributes to metabolic syndrome (2) (insulin resistance, screwy lipid overloads messing up the liver and arteries and being deposited as extra fat all over the body). The epidemiological effects of fructose’s role in the way our food is designed, produced and marketed to us are almost surely related to the high incidence of heart disease, obesity and type II diabetes in our population in ways that go beyond just a sedentary lifestyle. This inkling has been borne out by studies showing that HFCS/fructose-containing foods increase feelings of hunger and fat intake (1), and are related to increases in body mass index and frequency of obesity in children who drink too much pop (3).

The Corn Refiners Association ( likes to tell people in their FAQ that getting fat from sweeteners is your own fault, because everyone knows that sugars are fine for your health when “consumed in moderation as part of a balanced diet” and that “No single food or ingredient is the sole cause of obesity, but rather too many calories and too little exercise is a primary cause. Both sugar and high fructose corn syrup contain 4 calories per gram.” They also say that

“all caloric (nutritive) sweeteners (are) metabolized similarly… The body digests caloric (nutritive) sweeteners by breaking them into smaller units, primarily glucose and fructose. These “simple” sugars are absorbed into the bloodstream, where they are transported to the cells of the body and are then converted into energy. Though the individual sugars are metabolized by different pathways, this is of little consequence since the body sees the same mix of sugars from caloric (nutritive) sweeteners, regardless of source.”

The Corn Refiner’s Association happily glosses over the metabolic damage caused by regular HFCS consumption by referencing this article (4—which, by the way, references the 2004 Teff et al article, lol at the CFA) that shows how there is no difference between sucrose and HFCS consumption on 24-hour endocrine and metabolic profiles in lean women:

Is high fructose corn syrup metabolized differently than other sweeteners?
No. The myth that high fructose corn syrup is metabolized differently than other caloric (nutritive) sweeteners is based on studies that looked at pure fructose, not the mixture of fructose and glucose found in high fructose corn syrup. The most recent metabolic research published in the February 2007 edition of Nutrition found “no differences in the metabolic effects” of high fructose corn syrup and sucrose on circulating levels of glucose, leptin, insulin and ghrelin in a study group of lean women.”

Calling it “the myth” is, for one, false (unless glucose THE ORIGINAL SUGAR is somehow not a caloric[nutritive] sweetener) but at best completely missing the point, and trying to skirt around the fact that there’s plenty of fructose in both sucrose and HFCS. Guess who that research was funded by: Pepsico. Of course the Corn Refiner’s Association and Pepsico have about the same vested interest in demonstrating that HFCS has equivalent effects to sucrose—Pepsico finds it cheaper to sweeten that pop with the relatively low-priced HFCS from the CRA than sucrose and especially purified glucose. Plus, since drinking that pop doesn’t really make your body notice it has taken in food, you’re happy to have another one half an hour later when that ~45% glucose half of the HFCS has been used up. But while they love to use science to their advantage when needing to soothe the public (who has no idea that the chemical structure of sucrose contains almost as much fructose as HFCS and thus is like comparing apples to… more expensive apples?) both of them would of course much rather NOT highlight the science behind the clearly bad effects of so many money-making sweeteners in the diet of western people. Hey, maybe they all go golfing with the health insurance HMO scam artist criminals, having some hearty laughs and fist-bumps over how much money they’re all making off of our fat, stupid, lazy butts.

1. Teff KL, Elliott SS, Tschop M, Kieffer TJ, Radar D, Heiman M, et al. Dietary fructose reduces circulating insulin and leptin, attenuates postprandial suppression of Ghrelin, and increases triglycerides in women. J Clin Endocrinol Metab 2004;89(G):2963–72.

2. Stanhope, KL and Havel, PJ. Fructose consumption: potential mechanisms for its effects to increase visceral adiposity and induce dyslipidemia and insulin resistance. Current Opinion in Lipidology 2008, 19: 16-24.

3. Ludwig DS, Peterson KE, Gortmaker SL 2001 Relation between consumption
of sugar-sweetened drinks and childhood obesity: a prospective, observational
analysis. Lancet 357:505–508

4. Melanson KJ, Zukley L, Lowndes J, Nguyen V, Angelopoulos TJ, Rippe JM. 2007. Effects of high-fructose corn syrup and sucrose consumption on circulating glucose, insulin, leptin, and ghrelin and on appetite in normal-weight women. Nutrition. 23(2):103-12.

Managing your manager

It really makes a difference in your life if you can figure out how to manage your boss. That almost never means actually telling him or her what to do—most bosses do not take kindly to that, as one would expect. But being able to step outside the relationship, depersonalize the interaction and figure out which moves on your end are going to get you what you want is an invaluable ability. It can make the difference between a dysfunctional and a functional relationship, even if the other person is inherently dysfunctional themselves. In fact, some dysfunctional managers are the easiest ones to manage: they are so clueless when it comes to personal interactions and what really works that making them think things have gone their way (while actually getting your own) is REALLY easy. Like, you-feel-guilty-easy because they were so simple about it, but at least the thing turned out the way you needed it to. And some people greatly benefit from some outside, benevolent manipulation--manipulative behavior doesn't have to be a bad thing, it only becomes damaging when the big picture is ignored in favor of more personally selfish goals.

Sometimes it’s not so easy though, and the hardest part for women particularly is depersonalizing interactions to the point where you can control the dialogue. Interpersonal objectivity is hard for us girls, we tend to react to everything in relation to ourselves and how we feel about ourselves. If someone is an ass, it’s upsetting (uncontrollable fight-or-flight reaction)—you want to avoid interacting with them at all, and it is hard to stand up under a real-time assault and keep your bearings enough to know what to do about it. If someone is too nice, it can be really hard to get them to act on issues that require more hardassedness, and (if you’re not an ass yourself) to make sure they are getting the benefit of the outcome you want to make happen when they can’t. But with all kinds of people and all kinds of relationships, it is possible to move beyond the level of “how do I feel about this?” to “how can I make this person feel the way I need them to about this?”

Obviously there’s no list of rules or tips for this kind of skill, and some people just have an unconscious knack for it. But it’s not impossible to learn how to better control your situation and interactions, and it makes you feel like your life is more your own. Practice is the best way to get better at it, practice with an open mind to what you can learn from a bad situation.

"Are you women cold all the time?"

Yes, it is because we are female that 64 deg. F is not a suitable temperature for office air conditioning.

"Can't you just wear sweaters? Do you want to borrow my shirt?"

Surely it is our inappropriate styles of dress and our female condition that make the (awesomely mullet-ed) physical plant guys have to come adjust our AC temp from 64 to 70 deg F... it can't have anything to do with them being dumbasses.

I could have responded with "Are you older men always buying bizarre mullet toupees when your hair starts falling out? Couldn't you just shave your head? Do you want to borrow my blond She-Ra wig from Halloween a few years ago (because it would look less ridiculous than the beaver on your head)?" But I didn't.

Making the most of my startup

Ahhh, music to my ears: this very moment I am listening to my consultant lab manager have a conversation with a vendor about the upcharge VWR is putting on a big piece of equipment and driving him a hard bargain to get the price to match the lower one Fisher can get us for the exact same item.

And happiness is knowing I don't have to have any of those conversations!

We're trying an experiment: the woman who has been managing my PI's lab for the last couple of years is starting up a business as a "lab setup consultant." This lady knows her stuff, she knows all the vendors, reps, best quality discount supplies, how to combine orders to get freebies, and she is a tiger! She will hardball them and pit them against each other, all in the politest, sweetest conversational tone possible so they never know what hit them until they find themselves agreeing to throw in this or that extra, or take another N% off the already discounted price.

I am paying her far, far less than if I hired someone full time to just use about 1/4 of her time, with the added value of that skill and experience level, to help me make the most of my startup money for setting up my lab. She has already saved me thousands of dollars (even beyond the usual academic or institutional discounts) AND (this is the best part for me) she does everything so I can just focus on hammering out this last two months' worth of experiments to better characterize some of my systems while I still have everything setup in my PI's lab, and I don't have to have uncomfortable conversations or get upsold on the things I need. It's like having a personal shopper--the only decisions I have to make are about the particulars of things I am picky about like pipettor brand and 96-well filter plates (and, as pinus reminded me, big huge specialty items for which only I know what I want). I LOVE IT!!!!!!!!!111!!1!1!

Think about it: if I had to do all this myself, I would be spending at least 1-2 months almost full-time sourcing, getting quotes, ordering, setting up all of this stuff. For less than it costs to hire even a part-time technician, I get more value for money and my own efficiency is increased a hundred-fold. By the time I move, most of what we need to start doing work in the lab will be ordered and I will have been able to advance the current state of the technology by two months at high productivity ratio (postdoc time), rather than it taking us about six months in the new lab to get to the same point as we get in gear.

If anybody else starting up a lab wants her contact information, let me know. Hah.