SciCommTips episode 2 - Turn a colorblind eye

When preparing a figure for a presentation, manuscript, or proposal something to keep in mind is your use of color. I am a big fan of the use of color and shapes to help convey levels of meaning as well as in keeping themes consistent throughout projects. However there is one component of the use of color that is often overlooked, that is how your color choices can alienate a portion of your audience - the color blind, or rather color vision deficient. About 8% of men and 0.4% of women have a genetic trait that inhibits their ability to perceive some wavelengths of light, but a quick check of your figures can help ensure that they too can interoperate your work with the same ease as a color sighted person. In this episode of SciCommTips I will demonstrate an easy ways to check your images for color vision deficiency.




Please feel free to offer your recommendations on ways to improve figures to be more color vision deficient friendly. Or any stories you may have regarding data interpretation/misinterpretation due to color vision deficiency.

To learn more about color blindness
Colblindor has many great articles: http://www.color-blindness.com/2010/03/09/types-of-color-blindness/
Also this blog: http://www.testingcolorvision.com/what-is-colorblindness.php

Article about how to be color blind conscious in the sciences (includes microscopy and heatmaps)
Maxine Clark blogged in Nature Nautilus: http://blogs.nature.com/nautilus/2007/02/post_4.htm

Adobe soft proofing for color blindness
http://help.adobe.com/en_US/creativesuite/cs/using/WS3F71DA01-0962-4b2e-B7FD-C956F8659BB3.html

Some additional tools for checking your figures
If you don't have the Adobe CS4-6 there are alternative options to test your figures. Clobindor has a list of many options to chose from, including ImageJ: http://www.color-blindness.com/2008/12/23/15-tools-color-blindness/

Here you can upload an image and compare it under the various filters:
http://www.etre.com/tools/colourblindsimulator/
http://www.color-blindness.com/coblis-color-blindness-simulator/

SciCommTips episode 1 - How to move a figure from MS Office to Illustrator

Many scientists love to use Microsoft Office products for their work. Excel offers quick data organization and analysis while Powerpoint provides means to create figures for papers and presentations. However, sometimes the formatting limitations of these programs makes it hard to get the data exactly the way you want to present it. My personal solution is to take the figures and images I make in MS Office and bring them into Adobe Illustrator for final edits. How to do this is one of the most common questions I get when I present my data. I also find that I'm teaching my friends and colleagues how to do this with their projects. So what better 'how to' to start the Science Communication Tips (SciCommTips) episode series.

Learning to use illustrator can be a daunting task. Research labs often use Adobe Photoshop to edit their images and figures for publication. But when they try to play in Illustrator, all of the skills that you learn in Photoshop no longer apply. Strange how two programs from the same parent company can be so different from each other. However, Adobe Illustrator is a useful program when it comes to presenting scientific data as the clean crisp continuity of vector art creates a firm polished end product. Vector graphics are useful in that they are infinitely scaleable without loss of resolution, making it easy to adjust a single figure for multiple purposes. Plus, the MS Office graphics engine produces vector art for its shapes, smart art, and charts.

In this episode I will take you through the process of creating a new figure in Excel and how we can make adjustments to then import it into Illustrator without much hassle of learning advanced Illustrator techniques. This same tutorial will apply to Powerpoint figures, although I may revisit it in a future episode.

Please feel free to comment below. If you have any questions or recommendations about this tip or if you would like to see additional tips please recommend them in the comments section or direct message me on twitter: @liveinsymbiosis 

Video is on my youtube channel: http://youtu.be/t6bLwgwvX3I

Episode Notes:

Software used: MS Excel 2011 (Mac) and Adobe Illustrator CS6
Note: This tutorial should work on any version of Adobe CS and MS Office

Some of the Illustrator shortcut keys used (mac, sub 'Control' for PC):
Command+C = Copy
Command+V = Paste
V = Selection tool
A = Direct selection tool
Z = Magnifying glass
Command+0 = zoom to fill window
With selection tool hold 'alt/option' key click and drag to create a duplicate of an object

The dataset is from McNulty et al., 2013 PLoS Biology: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001637;jsessionid=22636C4DDB0793F5E87F85D0D612FB8B#s4

Round Table Discussion on the Hologenome - Google+

The Bordenstein Lab is about to host a round table discussion on the hologenome. I will live blog it as well as host one of the live feed videos here. The original link to the Google + page, where we will announce future updates and discussions.

Only 12 min before the life feed begins on the hologenome.

10 am Time to start!!!

@ 10:0 we have 8 participants so far and 10 viewers... if you can't join the hangout, you can still participate in the chat

@ 10:09, it begins!

@ 10:10 What, who, and  why of the hologenome. Some of the terms are supper organism, holobiont. The idea that the hologenome is still controversial and is an important discussion to have so all areas of biological sciences.

@ 10:12 Is the holobiont/hologenome jargon?
is it any different then any other organism-interaction?

Mark Martin

10:18 AM

Thought: microbiome is clearly coevolved and specific. Winnowing from much more complex environmental community. Two sides of one coin.

@ 10:19 is the host really any different than a single additional organism that is part of a continuum?

@ 10:21 What is the experiment needed to validate or deny the hologenome?

@ 10:27 what does evolution see? are the interactions negative or positive or are the windows of evolution and selection not able to fit within the trajectory of microbiome-host interaction?

@ 10:34 perhaps functional genes are perhaps important role in who and what are present as a hologenome.

@10:41 Bordenstomics! the hologenome needs more metaomics to be able to answer some of these questions.

@ 10:47 is it necessary to call the microbes anything different then the environment? or is it because there is a biotic factor of the microbiome that separates it from the abiotic factors?

@ 10:50 how is a tapeworm different then the microbiome?

@ 10:54 is the hologenome a useful phrase for the body of knowledge we have now? The microbes are not individual players but interactions that compose the species that we describe.

@ 11:01 we are wrapping up the discussion. It will be saved and uploaded to youtube.

Overall the discussion went really well. I didn't get a chance to copy in some of the chatroom posts (not fully caffeinated yet). But there were some really great discussion point brought up overall. Including the fact that a species and its microbiome are integrated into eachothers' success.

To summarize, the biggest component of the hologenome discussion was how should we define the hologenome relative to our existing concepts of evolution, species, ecology, and microbial ecology. Is there a distinction between the microbiome in a host organism as part of the host, or is the host just part of the microbial community? Clearly the environment plays a role in establishing the taxonomic representation of the microbiome but is it limited by the host? How is it truly different than any-other organism-organism interaction? The field of clearly needs to conduct more scientific investigations of the hologenome concept before we can address these issues. There was a general consensus that the term 'holobiont' does describe the unit of selection, but how far that extends beyond microbe-host interactions is still controversial.

The hangout consisted of mostly pro-holobiont supporters but David Baltrus was a wonderful foil for counterpoints to the hologenome. Arguments that the hologenome could extend to parasites like tapeworms, pathogens, and domesticated plants, where would they fit into the definition? These are great points that are an important dialogue to the discussion. He laid out a few additional components in a great blog post about ecological epistasis.

In the end, we all agreed that the round table could go for a round two. In the mean time, watch out for falling coconuts, you don't want to end up a statistic. 

The Mortal Life of HeLa

Henrietta Lacks and her husband David in 1945. Lacks Family Photo

Henrietta and HeLa

HeLa cells have been in the news recently. The oldest, and most commonly used cell lines around the world have had their genome sequenced for a second time. This cell line has been valuable to the progress made in human medicine in the past 60 years. But there is an ethical issue that has only recently been addressed. The HeLa cell lines came from a human, who has living relatives. Although these cell are now disassociated from the body, they still contain the same genetic material that is found in the family left behind.

In 1951, a 31 year old African-American mother of five checked into the Johns Hopkins Hospital after feeling a lump in her lower abdomen and experiencing heavy bleeding. Her life was running short but her legacy would unwillingly live on. Her name was Henrietta Lacks, and she was diagnosed with cervical cancer. It was unusually aggressive cancer that doctors had taken a sample of and began culturing it as a free living cell line. However, they did not ask Henrietta for permission to take her cells for scientific research. As she approached the end of her life, she would die never knowing that her cells were going to live on in laboratories all around the globe as HeLa. It was not until the 1970s that her family would even know that a small part of Henrietta was still alive.



Restoration of HeLa to Henrietta

There is a photo available on Wikipedia's creative commons site that I have seen used in the recent media frenzy. It is the cover photo of this blog entry, where a sepia toned ragged photo of Henrietta and David are handsomely dressed for a photo. This remarkable photo of the young couple has been tattered, torn, and taped. I have seen this a lot with older photos, though they are precious to the family, but sometimes time damages those keepsakes. Photo restoration has been a hobby of mine since college. I usually do them for friends and family but this photo of Henrietta and her husband is so endearing I had to try my hand at restoring it. You can tell how happy and proud she is to be there taking that photo, dressed so nicely, and 9 years before her diagnosis. I am providing the restored photo here, but the resolution of the image made it hard to do the best possible job. If I had a better scan of the original I think that I could get it even nicer. If anyone knows the Lacks family, I would like to send them a copy of the restored image. At the bottom of this post is a video of the restoration process that I did. It is not instructional as it is a time laps video of me working. The ability to restore this image, for me, parallels the restoration of HeLa's humanity to Henrietta, the woman who did not know she would save so many lives.

The restored photo of Henrietta and David Lacks

HeLa Now

The importance of Henrietta's contribution to science is vast. With tens of thousands of research articles using the cells for scientific research, her cells may be the best understood example of human biology. Her family on the other hand were unable to stop or conceal anything about themselves. Henrietta had become public domain. Any scientist could get her, do what ever they wanted to her, and not have to conceal her identity or that of her kin. This was a gross ethical oversight which only came to light long after Henrietta's death. In addition, her family was left without any compensation for the vast commercial gains made off of Henrietta's cells.

Although progress has been made in patients rights and consent in scientific research, HeLa still is treated more as a tool then as human. The recent Nature article publishing the HeLa genome did not consult the Lacks family. This means that genetic information about Henrietta was publicly available and inferences could be made about her family without their consent. I think that open access is important in science, but anonymity of a patient (involuntary as she may have been) is important too. The genome of the HeLa cells is a valuable resource to researchers but consideration to the family still needs to be maintained.

Recently the family was invited to meet with Francis Collins, the director of the US National Institute of Health, so they could discuss how to handle this new information about Henrietta. An interesting result of this meeting is that the Lacks family will now be part of the oversight committee that will evaluate proposals to use the genome. The publicly available version of the genome was removed and access is granted only to researchers whom can justify its use. This is a great benefit to the family, now they have some control of how Henrietta's cells (genomes) will be used. The ethical implications of patient samples and information is an important issue in today's society. We as scientists can gather more information about a person then ever before. But how we use, distribute, and protect the individuals rights are important in considering the future of medicine. If only Henrietta could have known how she would live on, how her family would be impacted by her life, perhaps things could have been different.

Photo restoration video

For more information on Henrietta's life and her cells:

• The book "The immoral life of Henrietta Lacks" by Rebecca Sckloot is a great read. Rebecca interviews the family and provides a perspective of the historical, ethical, and emotional aspects to Henrietta and her family. 
• The Radio Lab podcast "Famous Tumors" from May, 2010 is a great listen. Rebecca Sckloot leads us through an auditory journey with the HeLa cells, in addition to other great tumor stories that Robert Krulwich and Jad Abumrad walk us through. 

For more information on the recent developments with the HeLa cells and the NIH as well as the ethical discussion surrounding it:

• NPR's Michaeleen Doucleff wrote a nice synopsis titled "Decades After Henrietta Lacks' Death, Family Gets A Say On Her Cells" This is where I first saw the picture of Henrietta and David.
• Nature had a news article related to the story by Martin Bobrow "Balancing privacy with public benefit" that points out some very interesting aspects to the debate.
• Nature also had an editorial "Blood Ties"

Side note:

With such a low resolution photo it was hard to restore more without losing overall quality. Her eye and nose still do not look right to me so I'm going to work on it some more. But I hope that someone might be able to track down a higher resolution file for me to use.

Her family did not receive compensation for the profits companies made off of her cells. There is a foundation (http://henriettalacksfoundation.org) that is set up to help the Lacks family as well as those whom are in a similar situation.

Of pop art and holobiont

'Nasonia' by Robert M. Brucker, 2013. A digital homage to Warhol's 'Marilyn' series of screen prints.

We recently published the major part of my thesis in the journal Science -- "The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia."We were fortunate to be promoted to a Science Express article, which means that it is available online well before the final print, which should be around August-September (we don't have the final date yet). When we were in the process of submitting the final documents to the editor we included a few options for potential cover art. Although we may not be selected for the cover, the process did make me think about our work from an art history perspective.

It started when I called my mother, a retired high school art teacher. I asked her for recommendations for a visual way to represent the scientific story we were telling. She had come to my thesis defense, has heard me talk about my work, and has printed off my papers to put on their coffee table--she does not understand it all but she has a surface knowledge of what I do. After some thought, she recommended that I try imitating an Andy Warhol. I thanked her for her advice, but inside I felt that she did not quite understand what it was I was looking for in a concept image. I wanted something that could depict the complexity and the universality of the hologenome--the idea that the genome and the microbiome are linked in the evolution of any animal species. I could not see how nauseously vibrant screen prints was relevant. However, sleeping on it always helps me. The next morning, as I was brushing my teeth, it hit me--my mother was on to a deeper connection with my science than I realized. You see, Andy Warhol is one of the most iconic, great american artists, whom pushed the conventional boundaries of art into the familiar and ordinary. His work was pivotal to the Pop Art movement of mid 1950's-60's America. Much like the pop art movement, the hologenome theory is controversial within the field of evolution, yet it is easily connectable to our understanding of what makes a species.

For a little perspective, the pop art movement reveled in an anti-traditional and anti-esthetic means to present familiar everyday objects, events, and celebrities. Artists of this movement imitated the styles of commercial art and mass media to push away from the unfamiliar and almost-elitist abstract expressionism movement (artists such as Jackson Pollock). The tradition of art before the pop art movement set the artist and the concept behind the artists work as a superior form of experiential being, an expression of human emotion that was meant only to be reviled through exploration of the work. Pop art on the other hand was obvious, mashing every day objects and the emotions attached to those within the artist's piece. This push towards the common connection between the art and the viewer challenged the definition of what Art is. Since Art can now include the common and the surreal, connect emotion to the mundane, then Art can be almost anything. For example, Warhol's soup can prints represent the disposable, mass-produced American life of the era, but also something that has a life of its own.

The hologenome theory of evolution includes the microbial organisms as an extension of the host's genes. This theory is a concept that challenges the definition of a species, pushing it beyond the boundaries of the cell wall. The traditional understanding of a species are the gene-gene interactions between DNA and/or cytoplasm (mitochondria and chloroplasts) that limit the reproductive success between species. This has been the dogma of evolutionary biology for nearly a century, and with good reason. Gene-gene interactions likely the primary mechanisms that isolate species; however, there is a greater genetic diversity within a species if one includes the genes found in the microbiome. The expansion of available genetic diversity within a species provides new opportunities for selection to drive speciation. The presence of microorganisms is common and required for the health and development of the host organism they live in/on.

We take for granted the omnipresence of the microbes around us. Their life is as much apart of our own existence, but yet, until the hologenome theory, they played little part in our understanding of species. The same is true for our dependancies on consumerism and the celebrated individual as an unavoidable part the modern society but was not a part of our artistic dialogue until the pop art movement. Bacteria are often considered part of the environment, and any influence they have on a species is no different then any other organism-organism interaction, like say a predator and prey. But because it is impossible to have a naturally occurring organism without any microbiome, bacteria are essential to the existence of that species. Pop art parallels this, ordinary objects and pop culture references where not considered high art because they were part of everyday society, but yet art is a reflection of our society--neither exists with out each other. Our microbes are as much part of our identity as a species as Marilyn Monroe. The art and beauty of living surrounds us, though in mass produced quantities it represents what we are and where we are going.

For more information on the hologenome topic:
This video by Richard Jefferson on the definitions of the hologenome
A review of the hologenome thory by Eugene Rosenberg, Gil Sharon, and Ilana Zilber- Rosenberg.
Our review article, Speciation by Symbiosis giving examples as to how bacteria influence barriers between species (pdf).
Seth Bordenstein has written/vloged about the hologenome and speciation by symbiosis.

3MT and 10,000 views

After my dissertation defense I realized that the live feed was actually not of my powerpoint slides but the isight camera on my computer. Sorry abou that, 50+ min of me infront of the camera talking was not what I had in mind. I am working on uploading the slides with the audio of my defense, but in the mean time I have something much more digestible.

On March 22, The Graduate Student Council at Vanderbilt University held its first Three Minute Thesis (3MT) Competition. The 3MT stated at the University of Queensland as a means to have graduates students develop the skills to effectively explain their research to a general audience, in three minutes. If you have a few minutes to spare, check out some of their presenters from this year: here. The competition has spread throughout Australia and New Zealand. The finalists are really impressive and worth the 3 minutes of their video.

Vanderbilt is one of only a handful of universities in the US that is holding 3MT competitions. I submitted my abstract and was one of the 72 selected semifinalists. So, only a few days after my actual defense, I was condensing my thesis into a short three minute segment.

The rules were fairly straight forward.

1. Only one static (no animations) powerpoint slide
2. You only have three minutes to speak, if you are one second over you are disqualified
3. No costumes, props, or music

Really it is just you, standing there giving your 'elevator' pitch.

I really enjoyed my time at the competition. The quality of presentations were really top notch. I'm not sure if if the grad student council recorded any of them, but perhaps they will start doing so in the years to come. In the mean time, I recorded my 3MT for people to see. I would welcome any feedback on how to improve it. Please feel free to leave comments on this post or on the youtube channel directly. 

Jump to the 5:55 if you just want to hear the 3MT

http://youtu.be/XqXJHRmSXUw

Also, I have received over 10,000 views to my science illustration pages since June of 2012. That's really cool! I appreciate all those who have looked through my work. I have received several requests to provide instructional posts on how to do some of the illustrations and art. So, in the next few week I will be planning out some instructional videos of this nature--a how to communicate science and science art. Also, I will be going over some of the tools and tricks I have found useful in programs like PowerPoint, Excel, Illustrator, and Photoshop.

Dissertation defense LIVE! March 19th at 1:30pm CST

I was trying to find a way to have my defense broadcasted so that those of my family whom can not make it to my defense would be able to see it. I figured that since I'm streaming it, I could open it up to all those who are interested. So here is how this will work. Google hangouts allows for live streaming directly to a youtube channel that anyone can visit and view. Below are the instructions on how to view it.

1) Go to my youtube channel

http://www.youtube.com/channel/UC6H-Tqd3aqOhcXw3gzzvoAw

2) Click on the entry titled "My Dissertation Defense 3-19-2013 Vanderbilt University" This entry will be posted only an hour before my scheduled defense at 1:30pm CST.

3) This entry will be live streaming when I begin my defense, it will be of the powerpoint slides itself with my voiceover. Note that it will not begin playing until the start of my defense. Also, there is a slight time delay of 3 seconds or so. You may need to refresh your browser if it does not start within the first few minutes past 1:30 CST.

4) After the conclusion of my defense the video will be posted on my youtube channel that you can view at your convenience.

5) If you have any questions during or after my defense you may ask them via twitter, (@liveinsymbiosis), e-mail (bruckerm@gmail.com), or leave comments on my blog (http://liveinsymbiosis.blogspot.com) and I will answer them; either live or after my defense (most likely after the 20th).