Sorry to disappoint you but in biology and health there is much more than meets the eye.

Your genetic heritage might indicate that your have more chances than usual of developing a disease, but there are many other factors that will contribute to this finally occuring.

Metabolomics studies the footprint of these factors in order to give a more accurate picture of your condition.

In this post you will find what is metabolomics explained in simple words and with examples of application areas.

Metabolomics in simple words

Metabolomics surveys the metabolites that are present in organisms.

What are metabolites?

Metabolites are small molecules, smaller than genes or proteins. They are involved in metabolism as intermediates or products of metabolic processes.

Human examples of metabolites are hormones, amino acids, lipids, vitamins, and antioxidants, among others. Not only humans have metabolites, in fact all live beings need metabolites for their functioning.

Metabolites are responsible for the taste of tomatoes, the smell of plants, the color of fishes, and the poison of spiders.

Why is metabolomics useful?

Metabolomics describes the phenotype of an organism, which quoting Wikipedia is:

the composite of an organism’s observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird’s nest).

Phenotypes result from the expression of an organism’s genes as well as the influence of environmental factors and the interactions between the two.

The presence or absence of metabolites (and their concentrations) describes the state of an organism.

A practical application of this definition: Metabolomics can also describe the metabolic signatures of disease versus normality.

Imagine two identical twin brothers (who share almost identical genes). One has a stroke at 45 while the other lives healthy till he dies at 90. How can this happen if they are almost identical? Easy, lifestyle.

Can you guess who was having 2 meals a day at McRonald’s?

If you would have used metabolomics to check their lipid profile, you would have seen that the one with the stroke had a LDL cholesterol level abnormally high.

Examples Of Metabolomics Research

Metabolomics has proved useful to answer biological questions, for instance to determine the effect of a clinical intervention (aka, if I do this to these people, what do I see?) or to unravel the mechanisms of disease, to name a few.

If you are wondering what is metabolomics doing in the real world and what kind of biological questions metabolomics can answer, check these two examples.

How can I make my tomatoes tastier?

Imagine a company that sells tomato seeds want to improve their tomatoes in terms of taste, texture, aroma, and other properties you could not imagine a tomato possess.

Here the company can have two options, either modify genetically the tomatoes or to cross different breeds.

Next, a panel of tomato tasters (you guessed it, taster like with wine) give scores for these properties of each tomato sample.

Now, remember that metabolites are responsible for the taste and other properties of tomatoes.

By comparing the metabolic profiles of tomato types that scored high and low in each property, one can discover which metabolites contribute positively and negatively to the quality of tomatoes.

Is this diet good for reducing cholesterol?

Since you are interested in nutrition and health, you are curious about which diet improves your cholesterol, this is, bad cholesterol goes down, good cholesterol goes up.

The study is designed as follows: 4 different diets plus an extra control diet are chosen. You select 5 groups of people and each one gets a diet.

After some weeks, blood samples from the participants are collected and measured to determine the concentration of different cholesterol metabolites. And there you have your ideal diet to improve you cholesterol levels.

Sounds simple, huh? In fact, this kind of research, if you want solid results, requires a joint effort of many research centers and hundreds of participants.

Check this research about the best diet for  weight-loss maintenance.

Their goal was to decide which combination of high/low protein and high/low glycemic index was the, so you avoid the “rebound effect” (spoiler alert: the best diet is high protein and low GI).

Future Directions Of Metabolomics

Single Cell Metabolomics

Two individuals have different metabolic profiles if we measure their urine or blood. In the same fashion, different cell types in our body have different profiles.

In a not-so-far future, we will be able to extract a tiny sample from a single liver cell and compare its metabolic profile to the profile of a white blood cell, for instance.

By doing so, we will be able to focus on the specific organ or tissue involved in our research.

Metabolomics For Personalized Health

Have you heard of what 23andme.com is doing with gene analysis? you spit in a tube, send it by post and you get a detailed report on your genetic predisposition for a long list of diseases.

Now imagine the same, maybe instead of saliva samples with urine, but you will get a metabolic report, which describes your current health and if you are in any developmental stage of a disease.

If you want to receive future posts with new information on metabolomics, please subscribe to the RSS feed

This is me in Koh Chang (Thailand) during Xmas 2011 holidays

Dear readers, thanks for coming to my site. These are the 10 most viewed posts in my blog during 2011. I started to blog seriously from September 2011 and I am quite happy with the amount of readers I got in 3 months.

How To Identify A Social Media Douchebag

Most of those social media gurus/experts are in fact social media douchebags. Learn how to spot them and stay away from them.

The 4 Hour Workweek Guide To PhD Motivation

Boost your PhD motivation using the learnings from The 4 Hour Workweek. Finish your PhD faster. Increase the quality of your research.

Top 7 Things You Need To Know Before You Start a PhD

7 things you are not told before starting a PhD. Ignore them at your peril, you future PhD student.

Motivation Letter Example For PhD And Graduate Jobs

PhD motivation letter sample that you can use for PhD jobs. Use this cover letter for graduate school when applying for a graduate degree.

5 Phases of PhD Motivation Explained: The Roller Coaster Curve

During a PhD, graduate students go through 5 phases of motivation, here is how they work.

Free Template: Cover Letter Template For Scientific Journal Submission

Useful template for when you are submitting a scientific article and the journal requires a cover letter.

Top 42 Books For PhD And Graduate Students

From writing papers, to giving presentations, to grad school humor. The top 42 books for PhD and graduate students. Read them to survive grad school.

3 Websites For Alternative Income Generation As A Scientist

Generate alternative income as a scientist in your free time. Do freelance work using your expertise.

How To Use The Oxford Comma

How to use correctly the Oxford Comma when enumerating items in English.

Kill Procrastination Guilt With The Pomodoro Technique

Beat procrastination guilt and determine when a day was productive enough with the pomodoro technique. You might be more productive than you think.

Understanding and Classifying Metabolite Space and Metabolite-Likeness. 2011, PLoS ONE
Julio E. Peironcely, Theo Reijmers, Leon Coulier, Andreas Bender and Thomas Hankemeier.

Short Descritption Of The Paper

We have studied the chemical space of human metabolites.

We have built a computational model that assigns a metabolite-likeness score to input molecules.

We have studied which physicochemical properties and moieties are characteristic of human metabolites.

Long Description Of The Paper

This work describes the application of computational tools to predict the metabolite-likeness score of a molecule, i.e. how much it resembles a metabolite, and to acquire a global understanding of how the space of human metabolites is organized. In order to achieve this we made use of the state of the art in machine learning and the most comprehensive collection of human metabolites. To our understanding, we are the first to provide a metabolite-likeness score and to elaborate on its use for metabolomics, specifically in metabolite identification.

The use of computational models to classify metabolites and to compare them to other families of compounds has previously been published, but no prospectively validated papers have appeared.  The major contribution of the current work is threefold:

1. We employ and validate a variety of computational methods to not only predict if a molecule is a metabolite or not, but also to assign a metabolite-likeness score to molecules.
2. Three prospective validation sets are used to demonstrate the generalizability of our models and their applicability for drug research and metabolomics.
3. We investigate which physicochemical properties and chemical moieties are characteristic of the metabolite space.

We believe that our work would be of interest to medicinal chemists performing drug research, but specially to scientists in the field of metabolomics. Our aim is to show the metabolomics community how they can benefit from chemoinformatics.

Therefore, we devise further development and application of this work to accelerate discoveries concerning metabolite identification.

Calculate Metabolite-Likeness Of Your Molecules

If you would like to calculate the Metabolite-Likeness of some molecules, please contact me ( peyron #at# gmail.com)

Ditto if you want to know more about this work or to collaborate with me.

Image via Wikipedia

We all want to be somebody different. We all look up to someone we would like to imitate. There is so many people, me included, that feel inadequate, not good enough.

All what we want is to be better, improve ourselves. No wonder why self-help books abound in the New York Times’ list of Best Sellers.

The truth is that very few of us do something about it.

But what could be do? Can we just change ourselves automagically?

Well you can improve yourself if you want it really badly, if you feel enough pain.

It all starts by knowing what we want to change, what is it that we want to improve. There are lots of personality traits to work on and we need to focus. Focus. Focus. Focus.

It is not precise enough to say I want to acquire more good qualities and get rid of my imperfection. The key is to know what we want to acquire.

You need to define good and bad personality traits. And Warren Buffett has a great and simple (I love simple solutions) way of figuring out who you want to be.

As an example imagine you want to be more likable. This is, that people want to be around you, that they talk positively about you when you are not there. You want other to associate with you. This is to be a likable person.

Take 5 of your friends or people you deeply admire and describe what is the most prominent personality trait that you like about them. Is it that they listen well? Maybe they think first how to help you instead of their self interest? Are they positive in most situations? Why is it that you feel good when you are close to these people?

Write down their qualities of the people you like. This is what you want to acquire to be more likable.

Now take people you dislike, those that you have a bad gut feeling, those that you don’t want to hang out or make business with. Why is it that you don’t like this people? They don’t keep their promises? Do they look down on others? Are they energy suckers? Do they never speak up their mind? are they trying to be friends with everybody, thus making you not to feel special?

Write down the traits of those you dislike. This is what you want to get rid of to be more likable.

 It’s like switching your to-do and not-to-do lists, for a to-be and not-to-be list.

If you exercise enough the good personality traits, and remove the negative ones, you will turn into a much more likable person. 

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Being quite a procrastinator and a time wasting guy is not easy. Many times I feel guilty for wasting my time and my employers money. At least it looks to me I am wasting them. This procrastination guilt kept piling up day after day and the feeling was not a nice one.

When the end of the working days arrives, everything left is a bitter taste in my mouth that reminds me “I didn’t do enough today”. But even having so many unproductive days my bosses think I am still being productive.

How can this be? Are they using a different measurement?

Maybe just quantifying the amount of guilt I had after a day was not a good way to assessing my productivity. Since I tend to be quite hard with myself, perhaps I was doing a bit better than I thought.

Then it came to me, I should have my own way of measuring what a satisfactory day was. I didn’t want to lie to myself and not to base my satisfaction on other people’s opinion.

Basically I wanted two know:

I needed a way to answer two questions:

Has my day been productive enough? 

• So I don’t need to feel guilty.

Have I been so far today productive enough?

• So I can go home or start wasting my time guilt free.

And I found the pomodoro technique.

The Pomodoro Technique

• Work uninterruptedly and hyper focused for chunks of 25 minutes (pomodoros). If somebody/something interrupts restart the pomodoro,
• Take 5 minutes breaks between pomodoros and a 25 minute break after 4 pomodoros.

My goal was not to do a lot of pomodoros, but just to do enough pomodoros to be satisfied.

How To Get Rid Of Procrastination Guilt

Now when I start late my working day I know how many pomodoros I need to compensate in order to be happy.

The pomodoro technique is also useful if I want to spend part of my time on side projects, I make sure I have finished 6 or 7 pomodoros before hand. Then I can move onto something else guilt-free. It is that simple.

Now I cannot fool or punish myself anymore. And sometimes I surprise myself being more productive than expected.

Structure Generation, Metabolite Space, and Metabolite Likeness

Background

The chemoinformatics tools presented here are developed for metabolomics, specifically for metabolite identification. From our mass spectrometry experiments, and after data analysis, we want to identify certain metabolites of interest.

Of these molecules we might know the elemental composition (which and of how many atoms they are composed) and maybe one or more fragments (maybe a ring, a chain, or a functional group).

With this information we have to propose candidate structures for our unknowns. If we don’t find them in a database, we should generate the chemical structures with a computer tool, the structure generator.

Chemical Structure Generation

In this part of the talk I describe structure generator I have developed. It relies on the canonical augmentation approach proposed by Brendan McKay and it makes use of the Chemistry Development Kit (CDK).

The main use of this tool is: for a given elemental composition and prescribed non-overlaping fragment(s), it exhaustively produces all non-duplicate chemical structures.

Since the output list can be very large, we want to keep only those molecules that are likely to be metabolites. Therefore, we have developed a model that predicts the percentage of Metabolite Likeness of a molecule, this is, how likely a molecule is to be a metabolite.

Metabolite Space and Metabolite Likeness

We have combined 3 classifiers and 5 molecular representations to build metabolite likeness models. We wanted to see which combination could discriminate better metabolites from non metabolites.

The best models have been validated with a prospective validation set to asses that it can classify well new and unseen molecules.

We expect to use this model to rank candidate structures for unknown metabolites. Also, we hope these tools help scientist working in metabolite identification.

Image by cronicagastronomia via Flickr

A cook talking about innovation, in general? Can you learn something from a food maker? Well, if it is Ferran Adrià who shares his wisdom you can learn more than in MIT. Nevertheless, Ferran Adrià has revolutionized how topnotch (and not so topnotch) restaurants prepare their food.

Adrià is the owner of El Bulli, the famous 3 Michelin star restaurant that has been awarded the World’s best restaurant distinction 5 times. Well, for sure he can talk about success. What about innovation?

80% of the innovation in the culinary world of the last 20 years came from “El Bulli”

Now were are talking!!

Recently Ferran Adrià shared his views on innovation at the 50th IESE’s Global Alumni Reunion. For him innovation should come from simplicity and not complex processes and big budgets.

Innovation According Ferran Adrià

• Innovation does not require money, just ideas.

• Innovation is easier than it seems … That’s what small and medium businesses do … Hustle!

• Innovation is not a job: it’s a passion. You need ideas and to be bold.

• It’s not a matter of money. I am tired of listening to people using money as an excuse.

• We should teach our youth to be creative since early ages, but also teach them that budgets exist.

• At work you should over deliver. This is how things are. You cannot look at the print of a contract and say: this is as far as I will go.

• I am not Mother Teresa. At work I am demanding, I am tough … but I try to create a pleasant work environment.

• I don’t know much about cooking, just a bit more than you. I am fed up of seeing so many knot-it-all experts.

Diclosure

This post was originally written in Spanish (La innovación según Ferran Adriá) by José Manuel Alarcón. He kindly allowed me to translate it and post it in my blog. Gracias José Manuel!

From writing papers, to giving presentations, to grad school humor. These are the top 42 books for PhD and graduate students. If you want to survive in graduate school, you must read these books.

It is normal to feel lost in the vastness of a PhD project. Graduate school is a though place. You need to learn how to write, how to give presentations, how to do research, and how not to surrender.  And you have to learn fast.

Are you a graduate student that wants to know what (today’s) scientists had to do in order to finish at grad school? What they did to become good researchers? How come they didn’t go nuts in the process?

I expect this 42 books for PhD and graduate students to help in their quest for a career in science. Some of these books I have read myself or are in my to-read list. The remaining books have been recommended by very wise people that have survived and endured a PhD.

You will find all your answers in these books. If there is some missing gem, please let us know in the comments section.

Academic Writing Books

The Chicago Manual of Style, 16th Edition

A Manual for Writers of Research Papers, Theses, and Dissertations

How to Write a Better Thesis

Writing Your Dissertation in Fifteen Minutes a Day: A Guide to Starting, Revising, and Finishing Your Doctoral Thesis

The Literature Review: Six Steps to Success

Writing Your Journal Article in Twelve Weeks: A Guide to Academic Publishing Success

Merriam-Webster’s Collegiate Dictionary, 11th Edition

Dissertations And Theses from Start to Finish: Psychology And Related Fields

Academic Writing for Graduate Students, Second Edition: Essential Tasks and Skills

How to Write a Lot: A Practical Guide to Productive Academic Writing

On Writing Well, 30th Anniversary Edition: The Classic Guide to Writing Nonfiction

Presentation Skills Books

The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid

A Handbook of Public Speaking for Scientists and Engineers

The Visual Display of Quantitative Information

The Presentation Secrets of Steve Jobs: How to Be Insanely Great in Front of Any Audience

Even a Geek Can Speak

Presentation Zen: Simple Ideas on Presentation Design and Delivery

In The SpotLight, Overcome Your Fear of Public Speaking and Performing

slide:ology: The Art and Science of Creating Great Presentations

Confessions of a Public Speaker

Resonate: Present Visual Stories that Transform Audiences

Graduate School Motivation And General Advice Books

The Craft of Research, Third Edition

The Unwritten Rules of PhD Research

Mastering Your PhD: Survival and Success in the Doctoral Years and Beyond

A PhD Is Not Enough!: A Guide to Survival in Science

Advice for New Faculty Members

What They Didn’t Teach You in Graduate School: 199 Helpful Hints for Success in Your Academic Career

Getting What You Came For: The Smart Student’s Guide to Earning an M.A. or a Ph.D.

Advice for a Young Investigator

Surviving Your Stupid, Stupid Decision to Go to Grad School

Playing the Game: The Streetsmart Guide to Graduate School

Academics Handbook 2nd Ed

From Student to Scholar: A Candid Guide to Becoming a Professor

How to Survive Your PhD: The Insider’s Guide

The Smart Way to Your Ph.D.: 200 Secrets From 100 Graduates

Read This Before Our Next Meeting

Fun Comics

Piled Higher and Deeper: A Graduate Student Comic Strip Collection

Life is tough and then you graduate: The second Piled Higher and Deeper Comic Strip Collection

Scooped! The Third Piled Higher and Deeper Comic Strip Collection

Academic Stimulus Package (Piled Higher & Deeper)

xkcd: volume 0

5 Very Good Reasons to Punch a Dolphin in the Mouth (And Other Useful Guides)

Do you want to have an alternative income while working as a scientist?

Do you have some spare hours and you want to get extra bucks? Is your graduate scholarship not enough to pay for your lifestyle? Do you find exciting to work in different scientific and consulting projects in your free time?

The following websites will help you to sell your expertise and generate some alternative income as a scientist.

Innocentive

Innocentive is the meeting point for problem owners and problem solvers. You can change problems for “projects to be outsourced” and problem solvers by “smart scientists”.

A problem owner posts a challenge for which he is seeking assistance and provides a economical reward, which in many cases exceed 10K $ (not bad for alternative income). Some of these challenges require quite an effort and can should be performed in collaboration with other solvers.

Examples of challenges are: “Seeking Inhibitors of Fatty Acid Amide Hydrolase”, “How to Augment a Camera to Capture More than a Snapshot?”, or “The Cathode Ray Tube Challenge: New Uses for Recycled Glass”.

Acabiz

Acabiz is a similar concept to Innocentive.  This new website offers consulting opportunities to academic scientists within their field of specialization. Expect and alternative income per project in the range between 1K to 5K euros.

Currently, this new service has a large pool of knowledge holders, but not so many available contracts. Let’s hope that in the coming months we see an increase in the demand for experts.

Zintro

Zintro is general marketplace in which science is not the main area of interest. Here you can find anything from lawyers, to accountants, to mathematicians, you name it. In this sense, it is not far form other generalist  freelance websites like Freelancer.com or oDesk.com.So why you should consider Zintro?

If you check Freelancer or oDesk, the only scientific projects you can find fall in the category Scientific Writing. Fortunately, Zintro receives lots of project offers and best of all, you can describe yourself using a predefined set of keywords, which makes it easy to be found by potential seekers. As a matter of fact, I have been approached by people asking for advice in topics, which in many cases, were close to my expertise.

Room For Improvement In Freelancing Science

Truth be told, these websites still do not present a wealth of offers. Specially if you compare them with volume sites like freelancer.com or oDesk.com have.

I have discussed previously why scientists should consider freelancing as a valid career option. Unfortunately, these freelancing opportunities should come from other scientists and research companies, which might not be inclined to outsource their research projects.

Image by annais via Flickr

Finding topics for your posts

Sometimes it is hard to come up with topics to write in your blog. If you want to attract readers, these topics should interest them. How can you find these topics? Good old Google can help you.

In this post I will show you how I used Google Analytics, Google Trends, and Google Insights to find ideas for new posts and keywords. Furthermore, I will assume that one of your goals is to increase the number of visitors for your website.

Step 1. Google  Analytics / Webmaster Tools: What is your blog known for?

Google Analytics and Webmaster Tools allow you to check how well does your website rank for certain search queries.

Ideally you would want to rank as high as possible in Google Search in those topics that you are covering with your blog.

Since my blog is small and I cover many topics, my results are not spectacular. But If you check carefully, you can see that I rank well for “motivation phd” and “phd motivation”.

This tells me that if I keep writing on phd motivation I have chances of appear on the top results of Google and establish a reputation as expert douchebag in phd motivation.

Step 2. Google Keyword Tool: Are there enough searches?

Keyword Tool from Google Adwords gives you an estimate of the number of monthly searches keywords receive. Ideally, you would like to write about topics, i.e. keywords, that receive a lot of searches AND have low competition. Why low competition? Because it will be easier to rank higher in Google, which will bring more readers.

Here I see that in Keywords Ideas a word pops up, “graduate”. I realized that across my blog I was only use the word PhD to describe this research position. What about graduate? This word is the most used in USA for what in Europe we call PhD.

If I want to get more readers from USA I should also include “graduate” in my posts and my keywords.

You can also come up with new blog posts that use some of the suggested keywords. I did this with the Motivation Letter Example For PhD And Graduate Jobs.

Step 3. Google Insights: What are people really searching for?

With Google Insights you can check in detail search data, breaking down the searches by territory, date, and trending related searches.

What I want to see is what volume of searches received in 2011 certain terms in different areas.

Worldwide searches show me that effectively there are lots of searches that target “graduate”, so I should also include this word in my posts. It also seems that “advice” is a hotter term than “motivation”, so I should also use the former.
When I query for the same 4 terms in USA, I see that the only relevant is “graduate advice”. Same conclusion like above, since I want to get readers from the States.

What about India? They have an army of millions and millions of young university students, that might consider a Phd or graduate degree in science as a viable career path.

Here Google Insights shows that people from India mainly search for Phd and not graduate, so if I want to attract some of them, I should keep writing about PhD motivation.

What other tricks or tools do you use to generate ideas for your blog posts?