5 things you should know before dating a scientist

ORIGINAL: The Jayfk

by Editor-in-Commandant

January 10, 2012 

Journalist Tom Chambers has kindly provided a list of ‘5 things you should know before dating a journalist‘. While some might consider this list THE WORST THING EVER and that it HAS to be a joke, I think it could easily be adapted to scientists….

5 things you should know before dating a scientist

So, you’ve been eyeing that smart, attractive scientist you’re lucky enough to know personally. You’re intrigued. Your scientist is smart, funny, confident. Visions of Louis de Broglie or Rosalind Franklin putting on their safety glasses and lab coats to come to do experiments with you runs through your head..

Who can blame you? Science is a sexy occupation.

But scientists aren’t like the bimbos you usually pick up at the bar. Nor are they the assholes you ladies continually fall for. No, scientists are different beings (which is why you’re attracted to them in the first place), and you should realize — before jumping in — that this isn’t going to be a run-of-the-mill, boring, lame relationship you’re used to.

Here’s what you need to know:

1. We can figure things out. Understand, we’re paid to dig deep, find the secrets and wade through bullshit. We can pick up on subtleties, so what you think you are hiding from us won’t be hidden for long. Sure, we’ll act surprised when you eventually tell us you failed freshman biology in college — but we already knew.

We don’t take shit from anyone, so don’t lie to us or give a load of bullshit. We spend all day separating fact from fiction, listening to scientific supply sales reps and dealing with students’ bullshit. If you make us do the same with you, you’re just gonna piss us off. And don’t think we’ll be quiet about it. We’ll respond with the vengeance of an science blogger railing against some researcher’s recently-retracted paper — and we’ll enjoy doing it.

Just tell us the truth. We can handle it.

2. At some point, you will be a topic. For either a research project or blog post covering an area of research, something you’ve done or said will be the motivation. Get over it. Consider it a compliment, even if we’re arguing against you in print.

Think about it: we live our lives doing and writing about science. If you’re a part of our life, we’re going to do science on or scientifically write about you, your thoughts or a subject springing from one of the two.

Don’t be upset when an argument against your adoration of homeopathy turns up on our blog. We’re not directing the writing at you, personally — your ignorance was just our inspiration (there, doesn’t that make you feel better?).

3. Yes, we think we’re smarter than you. In fact, we know it. Does that smack of ego? Absolutely — but that confidence is what makes your heart go pitter-patter.

We have a strong, working knowledge of how the world works. That makes us great in conversation. We can delve into the intricacies of scientific laws, national and international research, where to find the good instruments, what’s happening with science fiction, what the good gamers are playing and more.

But there are pitfalls.

Guaranteed, when you say “evolutionary psychology” we will automatically say “bullshit” — “evolutionary psychology” is not science. We’re not trying to call you dumb (even though you don’t understand basic science), it’s habit. The same will happen when you say “causation” when you mean “correlation”.

We carry ourselves with a certain arrogant air. Embrace it (that’s what attracted you to us in the first place, after all). Don’t be surprised if we’re not impressed when you say, “I’m a scientist, too.” No, you are not. The fact that you sit in a coffee shop wearing @ThinkGeek t-shirts while reading @sciam does not make you a scientist. Nor does the fact that you “did some experiments in college” or that one day you want to “find a cure for the common cold.”

Look, we’re paid to do science. Every day. What’s more, our science matters. It changes opinions, affects decisions and connects people with the world around them.

We’re not spewing our data or trying to fabricate an aura of creativity. We study the real world — with real consequences.

Our research papers goes through three or four cranky editors who make us revise it before it’s printed a few hundred thousand times and distributed all over the world. You don’t do that unless you’re confident, even egotistical.

You may have some great notebook entries, scientific questions and rudimentary research ideas — good for you. Just don’t assume we’ll accept that as on par with what we do (unless you’re really hot, then hell, you’re a better scientist than I).

4. You’re not less important than the job — the job is just more important than anything else. One doesn’t become a scientist to sit in an office from 9 to 5 Monday through Friday.

We do take our work home. If science is happening, we’ll drop whatever we’re doing — even if it’s with you — to study it. We’re always looking for fundable research ideas, so yes, we’ll stop on the street to write something down, interview grad students or gather information for a grant.

On that same note, don’t get upset if you call us on grant deadline suggesting some afternoon nookie and we say, “I’ve got to put the paper to bed first.” That could mean hours from now, but we’ll have plenty of time to put you in bed later.

5. You won’t be disappointed. Scientists are intense, driven, passionate folk. We carry those same attributes into our relationships, making it an extremely fun ride well worth the price of admission. Our lives are never boring and each day is different.

If the pitfalls are scaring you away, consider this:

The fact that we’re inquisitive means we’ll listen to you. Even if it does seem like an interview, we’re paying attention to what you have to say (see rule No. 1).

We’ll write about you or your thoughts because you’re an important part of our life and we care about you (see rule No. 2).

Our brains are a great resource. Ever go on a date with an attractive person and wind up wishing you hadn’t because everything they say is just, well, stupid? That’s not going to happen here (see rule No. 3).

Yes, it may seem that we put the job ahead of you, but we’re driven. You’re not with that loser whose life is going nowhere and who’s completely content being mediocre (see rule No. 4).

There you go, five things you should know before dating a scientist. Feel free to add to the list, point out where I’ve missed something or leave a comment.

@DrRubidium Editor-in-Commandant

"Tree of Life" Technology Visualizes Complex, Biodiverse Relationships

ORIGINAL: Plant & Microbial Biology

By Karyn Houston, Plant & Microbial Biology

Scientists to develop groundbreaking new software

Scientists today deal with daunting volumes of data, and one of the most basic challenges facing researchers is how to organize that information into a usable format that can inspire new scientific insights. Now a nationwide team of university and private industry collaborators, including University of California, Berkeley plant biologist Chelsea Specht, have come up with a way to visually portray data so scientists can see, at a glance, how organisms are related.

It’s called “tree-thinking,” and the team will create a software package that will enable scientists and researchers to analyze data across the tree of life, enabling new evolutionary-based research to emerge that spans a tremendous range of fields, including medicine, public health, agriculture, ecology, and genetics.

The software will be developed with a $2 million grant from the National Science Foundation, shared by Specht and seven other university and private researchers in a unique collaboration to be announced this week. Taking available tools to a new level, the open-source software, called Arbor: Comparative Analysis Workflows for the Tree of Life, will be an intuitive interface based on visual workflows.

“With this application a researcher can identify patterns of molecular, developmental and morphological evolution, and then further explore those patterns and the processes driving diversification using novel analytical and visualization tools,” Specht said. “The visualization capacity of Arbor will enable researchers to study previously unrecognized phylogenetic connections across space and time.”

Analyzing on a Grand Scale

In this era of “big data” in science, the tree of life is evolving rapidly and dramatically. A “phylogeny” is the evolutionary history of the development or evolution of a particular group of organisms. We now have available large-scale phylogenies and massive amounts of data, including character traits, plant traits, mammalian traits and gene data, Specht said. Better software to be able to view that complex data is a must for scientists and researchers, with the lofty goal of being able to better understand evolutionary processes.

The software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators and students to analyze diverse types of comparative data on a grand scale. They will be able to see, at a glance, how organisms are interrelated and how they interact in geographical space and geological time. 

“Arbor will enable any scientist to address comparative questions applicable to crop improvement, human disease profiling, or developmental genetics – it will enable scientists from various disciplines to place their research questions into a phylogenetic context and use comparative tools to uncover novel patterns leading to new ideas on how to understand relationships or solve," Specht said.

The interface is a radical departure from existing software for comparative analyses. Building an Arbor workflow will have more in common with building a structure using Legos than with programming a computer. This will enable scientists trained in various fields of biology to harness the power of comparative evolutionary statistics to analyze their data in a sophisticated manner, generating easy to use workflows and publishable graphics.

Classroom Component

The new application will also have an outreach component.

The group included in the grant a module that will help K-12 teachers show “tree thinking” and enable them to take that next step with their students to envision and analyze data. They will be working closely with Judy Scotchmoor, assistant director at the UC Museum of Paleontology, to develop education-based modules and to provide support for training high school teachers in using Arbor for teaching comparative biology and evolution to their biology classes.

In addition, graduate students and advanced undergraduates will be invited to “hackathons” where they can contribute to the development of Arbor workflows, and to week-long Arbor training camps aimed at training students in the utility of Arbor for analyzing phylogenetic patterns and the role of geographic distributions, species interactions, or community ecology and structure on phylogenetic diversity.

The total grant is for $2 million. The Specht Lab, in the Department of Plant & Microbial Biology in the College of Natural Resources at UC Berkeley, will receive $600,000 dedicated to training of graduate students and postdocs in comparative evolutionary biology.

A Unique Collaboration

The project brings together a diverse group of biologists and private industry experts working together on the project.

The Principal Investigators are:

• Luke Harmon, associate professor of Biology at the University of Idaho, is the lead investigator on the project. Harmon primarily studies ecological and evolutionary aspects of adaptive radiations. The Harmon Lab is interested in the causes and effects of both speciation and trait change, and how species interactions shape macroevolution.
• Chelsea Specht, associate professor and plant evolutionary biologist at UC Berkeley. The Specht lab researches the processes and patterns involved in the evolution and diversification of plants, particularly monocots. They focus on the use of systematic in comparative biology, and the evolution of development, comparative genomics and the genetics of interspecies interactions.
• Robert Thacker, professor of marine and freshwater ecology at the University of Alabama at Birmingham. Thacker uses molecular systematic to place studies of organism interaction in to a comparative phylogenetic context. He extensively studies sponges, and, yes – his name is Bob.
• Jorge Soberón, professor in the Department of Ecology and Evolutionary Biology at The University of Kansas. Soberón documents and researches large-scale spatial patterns in the biodiversity of terrestrial species. He extensively uses databases of specimens from scientific collections or observations along with Geographical Information Systems software and he is currently a Vice Chair of the Executive Committee for the Global Biodiversity Information Facility (GBIF).
• Curtis Lisle is the CEO of Knowledge Vis, a company that specializes in custom software solutions for scientific and medical visualization. The Florida-based small business uses interactive computer graphics visualization and novel software and data management strategies to assist clients in data analysis and decision-making processes.
• Wes Turner, Technical Leader for Kitware, a software company that creates and develops open-source software that provides visualization, computer vision, medical imaging and data publishing to a variety of academic and government institutions as well as private businesses.
• Charles Hughes, Pegasus Professor in the Computer Science Division of the Electrical Engineering and Computer Science department at the University of Central Florida. Hughes is also the Director of the Synthetic Reality Lab and Professor in the School of Visual Arts and Design. Hughes is interested in digital puppetry, human-technology interaction, mixed and virtual reality, computer graphics and the theory of computation.

The core members of the group met at an NSF-sponsored AVAToL workshop last year and developed the idea for the grant to create the Tree of Life analysis & visualization software at that workshop. AVAToL stands for Assembling, Visualizing, and Analyzing the Tree of Life. Drs. Turner and Hughes were asked to join the group to provide support in the areas of large-scale computational analyses and visualization.

The first version of Arbor is scheduled to be released later this year, with updates and expanded operations to continue over the course of the three years of funding.