Tag Archives: biology

Field trip at the Chicago Field Museum!

2 Apr

I took a little break before attending two conferences to visit the Field Museum of Natural History in Chicago. Personally, I am a huge fan of natural history museums in general. Job-wise, it is an opportunity to see what kind of demonstrations and interactive elements museums incorporated into their exhibits. I simply could not miss the opportunity to visit the Field Museum.


The Field Museum was originally born as the Columbia Museum of Chicago after the famous World’s Columbian Expo on September 16, 1893. It was later renamed as The Field Museum after Marshall Field, the owner of several department stores in Chicago at the time and the major benefactor of the museum when it was first founded. The Field Museum is one of the largest Natural History Museum in the US. It hosts over 24 million specimens and objects, and attracts more than 2 million visitors every year. I was told that at any given time, we see less than 10% of all the specimens available at the museum. Pretty impressive.


The Field Museum has a large collection of specimens

Some students visiting the Field Museum. The kid in the photo totally photobombed this :)

Some students visiting the Field Museum. The kid in the photo totally photobombed this haha.

Here are some highlights for me:

Sue the T. rex – Sue is a famous Tyrannosaurus Rex skeleton at the Field Museum because it is the most complete T. rex skeleton discovered to date. “It” (the gender of the T. rex is actually unknown) was named after its discoverer  Sue Hendrickson.

At the Field Museum with Sue

Photo in front of Sue!


Sue’s skull weighs 600 pounds, which is too heavy to put onto the full skeleton, so it is actually sitting in a glass cover on the second floor balcony.

The Evolving Planet Exhibit – The Field Museum very wisely incorporated all the dinosaur skeletons into the Evolving Planet Exhibit, so we get to see how dinosaurs and us all fit together in the grand scheme of evolution. Some natural history museums failed to do so, and for me it doesn’t quite make sense to just see all the skeletons in one room without knowing how they are part of the earth’s history. Well done, Field Museum!

I see that someone is having a fascinating time with exhibit...

I see that someone is having a fascinating time with exhibit…

Inside Ancient Egypt – This exhibit is in the basement of the Field Museum (how fitting haha!). It hosts a collection of mummies, as well as the interesting diorama of mummy making…



Wonders of the 1893 World’s Fair – The Columbia World’s Fair hosted 65,000 exhibits in ~200 buildings to celebrate Columbia arriving in America 400 years prior. It was considered the event to see in a life time, and many spent all their savings just for a ticket to the fair. After the World’s Fair, some exhibits remained and became part of the Field Museum collection today. You can find highlights of the exhibit here on the exhibit website.

Using New Technology – Some cases have a QR code, which you can scan with your smart phone for more information. You can also download the museum app and design your own museum tour. Did I mention that there was free Wi-Fi in the museum?

QRCode  MuseumApp

Museum Discount Days – It turns out that Illinois residents can visit several museums and public attractions in Chicago for free on specific days. If you have read my post about museum admission fees, you would know how much I appreciate these discount days can do for science education and outreach.


The Brain Scoop – Okay, this is not really part of the physical “Museum”, but we (conference attendees) were invited to the Nerd Night Chicago before one of my conferences. I had the opportunity to meet Emily Graslie, the Chief Curiosity Correspondent of the Field Museum and the person behind the Museum’s Brain Scoop YouTube channel, in person!


She makes really cool “behind the scene” videos about the Field Museum. I highly recommend that you subscribe to the YouTube channel.

The Field Museum is definitely a must when you visit Chicago. I had an absolutely wonderful time there. Just make sure that you have plenty of time…especially if you are like me, who would attempt to read the descriptions for all the exhibit cases…


Pokemon + Biodiversity = the Phylo Card Game

25 Jul

For someone whose blog name was inspired by a Pokemon catchphrase, I am attracted to all things science & Pokemon. It therefore feels like my duty to talk about the Phylo card game. Even more importantly, there is a little back story here.

When I was still a graduate student, I spent a lot of time doing science outreach. One time, I attended an outreach workshop organized by the UBC Let’s Talk Science Partnership Program. This particularly workshop was led by David Ng, Director and Senior Instructor of the UBC  Advanced Molecular Biology Laboratory. Unfortunately, I don’t remember much from that workshop (sorry Dave!). But, one thing he talked about did stick with me. He mentioned a letter by Andrew Balmford and colleagues (you can read the excerpt here), who found that kids in UK could identify Pokemons (which are really just artificial “species”) better than identifying common wild life organisms. So – can we learn from this and come up with something that would help them discover real species and learn their names?

Little did I know back then, that this would soon be a new initiative led by David, and became a real game: Phylo, the trading card game. The game is much like the typical Pokemon trading card game you see kids play. The main difference? All the organisms on the cards are real. This is also an interesting artistic collaboration – there are some amazing art works done for the cards by many artists. Each card comes with the organism’s common name and Latin name, evolutionary tree info, key words, and more. If you browse the cards online, you can also read a bit more about each species.


What a Phylo card looks like. For more info visit: http://phylogame.org/game-play/

The Phylo game is an open access project – you can download the card deck online for free (!!) and print the cards on card stock. There are also special decks put together by the London’s Natural History Museum and the 2012 World Science Festival. If you are in Vancouver, the UBC Beaty Biodiversity Museum now produces  professionally printed starter deck with organisms featured at the museum, for sale at the Museum Gift Shop for $12.99. Proceeds from the sale will go to outreach and education activities at the museum. Online sale is currently not available, but you can sign up online to receive an email when online sale begins. Or, you can just download this starter deck here.

This touches on something else about science communication – how many other mainstream, unconventional ideas haven’t we tapped into for science communication and education? Something to think about…


Sockeye Salmon

How is gender bias in science studied? II. Learning from existing data

23 Jul

This is part 2 of my 4-part series about studying gender bias in science (See part 1, part 3).

For studies using existing data, we look at information that is already available, and learn from the information through data analysis. The difficulty in these studies is that because you are not in control of how the information came about, you cannot control all the different factors that can contribute to your results. Data analysis becomes very important.

The two papers I am reviewing in this post are about the percentage of female presenters at academic conferences. Why study gender bias in a conference setting? Scientific conferences are where scientists meet and share their latest research findings. The lack of women presenting at a conference results in low visibility of established female researchers. This could give younger female scientists the impression of the lack of women in the field and discourage them from staying in the field. In addition, gender bias could mean that we are missing out on outstanding research done by female scientists.

In 1911, the Solvay conference was attended by only one female scientist (Marie Curie). Are we doing better now?

In 1911, the Solvay conference was attended by only one female scientist (Marie Curie). Are we doing better now? http://en.wikipedia.org/wiki/Solvay_Conference

First, let’s look at Stag Parties Linger: Continued Gender Bias in a Female-Rich Scientific Discipline by Isbell, Young, and Harcourt, published by PLOS ONE in November 2012. In the study, data from 21 annual meetings of the American Association of Physical Anthropologists (AAPA) were reviewed and analyzed. The authors focused on the percentage of female scientists doing poster, oral (better than poster), and symposium (invited, better than oral) presentations on Primatology at the AAPA conferences. Immediately I had some difficulty with this paper, because the authors did not state up front exactly what their research questions and hypotheses are. It is hence hard to tell what they are analyzing, what they should compare the data to, and what I should consider important in the paper. I also have problems with their data selection criteria among a few other things. I will include that as supplementary reading at the end of this post for those who are interested.

The authors found that women gave significantly more poster than oral presentations, while for men this is not the case: Women – 599 posters vs. 313 talks; Men – 283 talks vs. 253 posters. Why? The authors suggested:

One possibility for the bias in favor of women giving posters is that it happens not at the self-selection stage but by others during the development of meeting programs. However, data on presenter requests and decisions from the program committee for the last two years show that men were 12% more likely than women to request talks over posters, although this difference is not statistically significant with only two years of data… In addition, men’s and women’s requests to present talks were denied at a statistically similar rate…  Nonetheless, non-significant trends in assigning posters to those who preferred to give talks (22% for men vs 29% for women) suggest at least the possibility of some additional bias against women occurring at the selection stage.

I am not sure how the authors managed to write this using 2 years of data especially when no significance was shown. If you have lots of data, perhaps it is possible to argue the trend – but data from 2 years cannot really tell us anything.

The most important figure and data analysis in this paper is Figure 2. In this figure, the authors tried to demonstrate that when the symposia were organized by committees with only female organizers, or by those with organizers from both genders, the percentages of symposium presentations with women as first authors (because typically the first author is the most significant contributor, and most likely the presenter, but this varies from field to field) are not significantly different from the overall percentage of poster and oral presentations with women as first authors – represented by the solid black line. What is striking is that when the committees had only male organizers, the proportion of presentations with women as first authors dropped significantly to 28.8%. 

Figure 2. Proportion of women as first authors of posters, talks, and symposia at AAPA meetings. The average proportion for all presentations with women as first authors over a 21-year period of annual meetings of the American Association of Physical Anthropologists is indicated by the solid black line. F-Org. Symp.: symposia organized by women only; F/M Org. Symp.: symposia organized jointly by women and men; M-Org. Symp.: symposia organized by men only. doi:10.1371/journal.pone.0049682.g002

Figure 2. Proportion of women as first authors of posters, talks, and symposia at AAPA meetings. The average proportion for all presentations with women as first authors over a 21-year period of annual meetings of the American Association of Physical Anthropologists is indicated by the solid black line. F-Org. Symp.: symposia organized by women only; F/M Org. Symp.: symposia organized jointly by women and men; M-Org. Symp.: symposia organized by men only.

There are several problems I can find with this analysis. First of all, I disagree with how the authors thought that career stage effects are irrelevant here.  The black line groups female presenters at all stages together – from perhaps undergrads, PhDs, all the way to established researchers. Typically, invited speakers are established researchers, so if there is a small pool of established female researchers to begin with, then the issue is with the lack of established female researchers (in itself, also a problem), not with the selection process (bias/discrimination). Secondly, the authors compared ratios based on the average from all 21 annual meetings. This is very risky, as a small number of years with large disparities could easily affect the overall average (granted, the gap does seem large). An average also does not reflect changes throughout the years (are things getting better/worse?). The authors mentioned they did compare the averages over 7 year increments – why 7 years? Would the results change if we choose another increment? This decision is very arbitrary.

In the end, the authors concluded that there is a gender bias against women in the field of Primatology. I personally don’t think that the analysis in this paper was done well. This is not to say that the authors were wrong, but bad analysis means that it is not possible to tell if the results indeed reflect reality, and bad analysis does not allow us to pin point the problem and discuss possible causes.

The next paper, Fewer invited talks by women in evolutionary biology symposia by Schroeder et al, published in the Journal of Evolutionary Biology just last month, was done much better! The authors analyzed data from the European Society for Evolutionary Biology (ESEB) Congress in 2011 (a recent meeting where all abstract submissions were accepted), and also from 2001-2011, looking at the sex ratio of presenters (poster, regular, invited, or plenary).  The authors right away talked about their hypotheses for the project:

We hypothesize that because the scientific achievements of women may be less visible than the achievements of men, female scientists may be overlooked more often for invitations to talk. If this is true, we expect the sex ratio of invited speakers to be biased towards males, even after accounting for career stage and the population sex ratio of the research field. The sex ratio of speakers at a symposium can also depend on the genders of the symposium organizers, with fewer women speaking in male-only organized symposia. We therefore expect that symposia organized only by men will have fewer female invited speakers than symposia that have at least one female organizer.

The authors started by establishing the two baselines for the purpose of comparison, hence controlling for career stage effect and presenter research quality. 1)  the faculty sex ratios from the Evolutionary Biology departments at the world’s top-10 universities for life sciences and 2) the sex ratios of first and last authors of research articles published in Nature and Science. Last but not the least, they also included the sex ratios of faculty in biosciences in the UK, and sex ratio of faculty in science and engineering across the EU, for comparison.

Looking at ESEB 2011 specifically, the authors found that the sex ratio of the plenary speakers (also invited, but plenary speakers are usually prestigious) did not differ significantly from the sex ratio of all other oral presenters, or from that of all regular speakers (presenters?). But, the sex ratio of invited speakers was biased toward men when compared to all other presenters and when compared to all regular speakers (the terms got a bit confusing here). The most striking discovery was this:

Although 23% of all initially invited speakers (including those that declined) were women, only 15% of the realized invited speakers were women. This reduction was because 50% of invited women declined talks compared to 26% of invited men…

This group also looked at whether there is any correlation between females in the symposia organizing committee and the percentage of female invited speakers:

There was no association between the presence or absence of female organizers and the respective sex ratio of their invited speakers, contrasting with the findings of Isbell et al.

Then, they started to look into the data from past ESEB congresses (2001-2011).

Randomizations showed that the sex ratio of realized invited speakers (15% women) was lower than baseline populations of early–mid career stage scientists (including first authors in top-tier journals), but similar to senior scientists (Professor and last authors in top-tier journals; (Fig. 4)). However, the 23% of initially invited speakers who were women (and of whom a larger proportion of women than men declined to speak) was lower than baseline populations of early–mid career stage scientists (Lecturers & Fellows) but did not differ from Professors or authors in top-tier journals (Fig. 4).

So some good news and bad news from this paper. Good news – the sex ratio of invited speakers at ESEB 2011 did not differ from that of Professors or authors in top-tier journals (so this points to the issue of a small pool of female researchers to invite from). Also, whether or not there are females on the symposia committee does not affect the sex ratio of invited speakers at ESEB.

Bad news – 50% of the invited female speakers declined invitations, leading to the very low number of final, realized female invited presenters. Why? Could it be how females tend to not like self-promotion? Have self-assessment bias? Maybe the problem lies with Child care (which was not available at ESEB 2011)? Lack of travel funding? Why don’t plenary speakers have the same problem?  The authors provided some references in their article that are worth reading.

It was enjoyable reading these two articles side-by-side, giving me a chance to compare how the two studies were done. I think the lesson for me  here is that the study of gender bias using existing data can get really complicated. It is important to make attempts to control other factors that might affect the results, instead of giving yourself arbitrary reasons not to do so. Also, studies like these are done for a specific field, and we must recognize that gender bias might exist in other fields that were not studied, such is the limitation of these papers.

Next time in this series, I will be reviewing: Science faculty’s subtle gender biases favor male students by Moss-Racusina et al, and The Matilda Effect in Science Communication: An Experiment on Gender Bias in Publication Quality Perceptions and Collaboration Interest by Knobloch-Westerwick, Glynn, and Huge. It will likely take me 1-2 weeks to write that up, so stay tuned!

Isbell L.A., Young T.P., Harcourt A.H. & Lambert J.E. (2012). Stag Parties Linger: Continued Gender Bias in a Female-Rich Scientific Discipline, PLoS ONE, 7 (11) e49682. DOI:

Schroeder J., Dugdale H.L., Radersma R., Hinsch M., Buehler D.M., Saul J., Porter L., Liker A., De Cauwer I. & Johnson P.J. & (2013). Fewer invited talks by women in evolutionary biology symposia, Journal of Evolutionary Biology, n/a-n/a. DOI:


Postscript 1: Here are some other reviews of the Isbell, Young, and Harcourt paper

I would also suggest that you read Athene Donald’s blog post All Male Invited Speakers? It’s Complicated! on the Schroeder et al results. The most interesting part is the discussions in the comment section (Athene tweeted about this and invited people to comment on the post/paper). 

Julia Schroeder and Deborah Buehler wrote a post about their results, Women’s contribution to science goes unheard.

Postscript 2: There are some additional anecdotal discussions on blogs regarding gender bias at other conferences. Unfortunately(?), in some cases, the discussion of the lack of women at conferences became a discussion of statistical methods. This further speaks to the difficulty and importance of properly analyze existing data.


Interestingly, not all AAPA presentations are included. They authors listed, in their methods section, their selection criteria:

  1. Include titles in sessions devoted to to primate behavours/ecology
  2. Exclude titles in sessions devoted to primate skeletal biology/evolution
  3. Exclude titles in which non-human primates were used only as models to address hominin behaviour or evolution
  4. But hominin hahaviour/evolution was included when looking at symposia

2 and 3 are because these areas do not have strong female representation (What does that mean? Is that a good explanation?). 4 is because “they are interested in the behaviour of the organizers than the relevance of the topics” (but wouldn’t that be interesting for posters and oral presentations?). The rationale is not clear to me, so at this point it feels a bit cherry-picking.

While the authors’ main focus was the American Association of Physical Anthropologists (AAPA) annual meeting, the authors mentioned results from other meetings (American Society of Primatologists, American Society of Mammalogists), which was really distracting for me. I wasn’t sure how data selection was done for the other meetings, and if the other meetings are also attended by the same pool of people.

How is gender bias in science studied? I. Surveys and interviews

9 Jul

Bias: [mass noun] inclination or prejudice for or against one person or group, especially in a way considered to be unfair – Oxford Dictionaries

This is part 1 of my 4-part series about gender bias in science (part 2, part 3). It is not a surprise that I am interested in gender issues in science. As one who has gone through graduate school myself, I have been curious about why many of my classmates decide to leave academia (note 1). As one who now works for a physics & astronomy department, I wonder why there are so few female students studying physics and astronomy, and why physics, the field as a whole, faces such difficult challenges in recruiting and retaining female scientists.

This is also a problem in science, particularly physical sciences.

This is also a problem in science, particularly in physical sciences. Source: “Piled Higher and Deeper” by Jorge Cham. http://www.phdcomics.com

The cause for the lack of women in science (particularly in physical sciences) is complex and still debated. This is probably why it is very difficult to come up with a specific strategy to deal with it. What I hope to do here is to look at how gender bias, a potential cause for the lack of women in science, is studied. Is it a problem, and if so how serious is it? What does research say? Is there something we can do about it? I will review a few articles written in the past few years – starting with this one that uses surveys and interviews to learn about male and female scientists’ perceptions of gender disparity in physical sciences. In the next few posts, I plan to talk about the use of existing data and well-designed experiments to study gender bias in science. Some of these studies are well done, while others are not. Some of them are misinterpreted generally. Even though each method of studying gender bias has its advantages and drawbacks, together they paint a picture of gender bias in science for us. And this is important – if we don’t understand the problem, how do we know what to do with it? And if we don’t know the scope of the problem, how can we allocate appropriate resources to it without taking resources away from other possible causes?

Because of my background, I am much more familiar with studies in physical sciences, not social sciences. On one hand, I think this good for writing these blog posts because I will be asking a lot of the same questions that you will be asking, dig into the bottom of things, and will be learning as I go. One the other hand, I might be missing something that’s so obvious for social scientists, or important articles on this issue. I invite everyone to be part of this conversation, and hope that I can learn something new myself!

1. Reviewing data from surveys and interviews

Ecklund, Lincoln and Tansey published their study, “Gender Segregation in Elite Academic Science” in Gender & Society last year (2012) (The article is accessible through the National Science Foundation! Well, at least I found the link hosted on their site). This study was based on data collected from a survey of 2503 scientists in physics and biology (graduate students to full professors). These two fields were chosen by the authors because while they are both core disciplines in science, the male to female ratios within these disciplines are very different. The scientists were asked to choose why they think the best explanation is for there being fewer women in physics than in biology (rephrased options): a) more natural ability in biology, b) preference for biology over physics, c) more funding for women in biology, d) more discrimination for women in physics than in biology, e) fewer mentors for women in physics than in biology, and f) other. 150 respondents were later selected for in-depth interview.

The majority of the people chose one of a), b), d), and e) – I counted about 70-80%  of them (few chose c according to the authors). 18.6% chose f). Interestingly, you can see from Figure 1 that about the same percentage of female and male scientists choosing a) natural ability and e) fewer mentor (there is more about this to come). On the other hand, there seems to be a gap when it comes to b) preference and d) discrimination – more men chose b) and more women chose d), especially those who are established female scientists.

It will take a bit more than just looking at the graphs to tease out the details. The authors used multivariate logistic regression to look more carefully at the survey data to see if the differences are indeed significant. I tend to get very nervous when it comes to the statistical analysis of multiple variables – because the it is hard to tell if the variants interact with each other or not. But we will set that aside for now.

Compared to senior male biology faculty (the omitted category), women at all career stages in physics are less likely to say that preferences explain the disparity between disciplines. Women faculty in both [physics and biology] disciplines are more likely to cite discrimination, while senior male faculty as well as male postdoctoral fellows are generally less likely to agree.

This also changes with the career stage a female scientist is in:

Conversely, the demand-side argument that women face more discrimination in physics is least supported by graduate students and postdoctoral fellows but gradually gain traction among faculty, particularly with women.

The authors cited several possible reasons. Perhaps there is a selection effect – that those who stay in academia happens to agree with the argument (so those who disagree with discrimination being a reason were selected out in the process of academic career advancement). Perhaps those who have stayed in academia for a while experience more discrimination over time. Or, perhaps things are actually better, so the younger scientists do not experience (as much?) discrimination as those who started out 10-20 years ago.

Information from the interviews provides some qualitative narratives to further illustrate what was found in the quantitative data analysis. What I find most interesting is that while the percentage of male scientists who chose “natural ability” and that of female scientists are similar, it appears that they might define natural ability very differently:

Scientists who are men talked about brain differences and mathematic ability while women scientists mentioned connecting with their subjects (meaning that women are better able to connect to the subject matter of biology, such as working with animals, versus the subject matter of physics, such as working with particles).

(By the way, if you plan to tell me it’s about mean/right-tail, biological sex/brain development/innate math ability differences, I refer you to additional reading on this matter. In short, it is BS, so please stop referring to this as the reason.)

When it comes to the matter of discrimination or discouragement, male and female scientists also have different perceptions. Male scientists tend to focus on what happens earlier on in a woman’s life, while female scientists tend to focus on the current environment.

Men were more likely than women to discuss these deficits in the educational system, explaining that socialization subtly discourages girls from taking physics classes.


It was predominantly women who identified the present-day structure and environment of physics departments as discouraging women from entering physics.

Last but not the least, while to me academia is academia is academia, some respondents actually pointed to the difficulty in balancing family and research in physics as a reason. It seems that something about physics gives people the impression that doing research in physics makes it harder to balance a family life.

Although these scientists argued that there may be something in particular about physics (compared to biology) that makes it more difficult to balance family life with an academic career, our survey data demonstrate that women scientists in both disciplines work approximately the same number of hours per week. […] This provides some evidence that career-family difficulties may not actually be unique to physics as a discipline, but rather that the perception of the structure of physics itself may cause tension between career and family responsibilities.

It is very interesting for me to read about how male and female scientists perceive the reason of gender disparity in physics and biology very differently – like a he said, she said story. The interview narratives gave us a lot more insights into this discrepancy in perception.

BUT, we do need to keep in mind that surveys and interviews are rather subjective. In fact, we cannot say from results of the surveys and interviews that bias and discrimination do or do not happen, as the perception of this might be different from the reality – thinking so doesn’t mean that it actually is so (but there are ways to determine actual bias and its effects – this is done in two papers that I will talk about in part III). Media, unfortunately, tend to focus on the words “bias” and “discrimination” and forget about what the study really says (see this, “solved the mystery?” I wish it were that easy. And this, and this by their public affairs office, with terrible headlines). This makes the already complicated issue even more difficult to tease out. For me, the most important message of this study is this: We should note the difference in perception by male and female scientists, as this difference might indeed contributes to the difficulty in resolving gender disparity in science. Furthermore, improving the perception of science and different fields of science, either by improving program structures or better promotion of the fields, could potentially encourage the next generation of female scientists to enter scientific careers.

Next week, I will be talking about two papers: Fewer invited talks by women in evolutionary biology symposia by Schroeder et al, published in the Journal of Evolutionary Biology just last month. And, Stag Parties Linger: Continued Gender Bias in a Female-Rich Scientific Discipline by Isbell, Young, and Harcourt, published by PLOS ONE November 2012. (Read part 2 here)

Ecklund E.H., Lincoln A.E. & Tansey C. (2012). Gender Segregation in Elite Academic Science, Gender & Society, 26 (5) 693-717. DOI:


It is difficult to figure out what cause the lack of women in science, and it is even hard to figure out what to do. Here are a few different points of views:

Additional reading about math performance and gender

  • The review by Ceci, Williams, and Barnett in 2009 went through great length to discuss sociocultural and biological considerations for women’s underrepresentation in science, digging into research results that I wouldn’t have thought to be relevant.
  • Janet S. Hydea,and Janet E. Mertzb reviewed available literature at the time (2009) in their article Gender, culture, and mathematics performance.
  • And, just for fun, how can we forget about Larry Summers’ comment about the lack of women in science *double-facepalm*(this comic is meant to be sarcastic, by the way!)

Larry Summer on Women in Science

I have a headache reading about ENCODE: moving into the realm of “big science”

28 Feb


I spent the past few days reading about ENCODE: the ENCyclopedia Of DNA Elements, which is generating a lot of fuzz right now – why does reading about it give me a headache? What is ENCODE? This is a great chance to talk about this “big science” project, and to learn how communication of scientific results can become a mess…

The genome is a collection of genetic codes, based on which an organism (like us) gets the traits and features the organism has. These traits and features come from many processes within the cell – the codes are transcribed and translated to become chains of amino acids, which are then modified to become proteins, which are then transported to where they need to be, and essentially become the building blocks for an organism. Now, after the Human Genome Project, we have an idea what the long sequence of codes looks like – 3164.7 million chemical nucleotide bases, each is represented by a letter of A, T, C, or G. This is massive! If we were to print this out letter by letter, apparently we can fill two hundred 500-page telephone directories. The ENCODE project (420 scientists, 32 labs around the world) aims to go a step further. It says on its project website:

The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

This is an important step, because simply knowing the codes does not tell us what they really do. But how do you start building a comprehensive list when you have 3164.7 million nucleotide bases to go through? In general, the ENCODE approach is this – let’s imagine that you are doing online shopping at ebay, which has lots and lots (and lots!) of products. Some are useful, working products, and some are not. You want to get a clock, but looking for it one after another is simply taking too long, so instead you look for specific “features” – something with gears, a circular face with numbers 1 to 12 on it, with hour/minute hands, and so on.

This is actually a pretty smart approach. In their 2012 paper, the ENCODE team looked for 4 features: regions of transcription, transcription factor association, chromatin structure, and histone modification, because these are elements that likely matter if we are to search for something specific (like, a clock) later on.

So what’s the problem? It mostly comes down to one word – “function.”

In ENCODE’s news release, they stated that

[…], researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions where proteins specifically interact with the DNA.

The news release further stated that “most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms.”

This sent a shock wave throughout much of the science community. From what we learnt about DNA and human genome so far, we know that a large proportion of the sequence is not “functional” – doesn’t code for a protein and doesn’t seem to have specific purposes in the cell. It is what we called “junk DNA” (terrible term, because not having immediate functions doesn’t mean that it should be thrown out – so many scientists avoid the term). 80%  is much, much higher than what was expected by most scientists. This discovery by ENCODE was picked up immediately by media, marked as “an overturn of the junk DNA theory” *cringe*. A new breakthrough in the field! – or is it?

Just because it has a gear doesn't mean it is something "functional" (image by Catherinette Rings Steampunk)

Just because it has a gear doesn’t mean it is something “functional” (image by Catherinette Rings Steampunk)

You might have figured out what doesn’t seem quite right here. What ENCODE identified were “functional elements” – elements that suggest the possibility for biological functions. Just like not all products with gears are actually “functional” (it could be a clock, a broken watch, some “as seen on TV” product, a bag of random mechanical parts, or a craft project glued together by your 4 year old nephew), identification of functional elements does not equate to actual biological functions in your cell. And having functional elements does not confirm involvement in critical cellular pathways or association with important functions in the cell.

After the immediate media hype, other scientists expressed concerns (to say it lightly), but it was too late (read A Genome-Sized Media Failure by Michael White). This also leads to a very recent, rather aggressive paper by Graur et al refuting the claims by the ENCODE project. This whole thing is now very messy (that’s why I was having a headache) 😦  I won’t elaborate much further, but if you want to know more about this – see Further Reading.

The funny thing is, ENCODE could have been more specific, could have chosen a less controversial term –  like “specific biochemical activity” as suggested by PZ Myers, or perhaps “ability to bind to cellular factors.” If they did not attempt to over-reach the claim,  the focus would have remained on the amazingly huge amount of information that ENCODE provides, which can now be analyzed by scientists around the world to enable us to know more about our genome and how it works.

The ENCODE experience is probably good for science (I didn’t say it is going to be a pleasant one…). We now have this enthusiasm/obssession about big science, that there is so much pressure to get the “next breakthrough” out, to create the next hype. But we should really come back to the objectives of these big science projects – for ENCODE, it is about building an informative genome database for scientists – and disseminate well-supported information to the public and media with adequate explanations.

And, scientists or not, we should remain curious yet inquisitive about “breakthrough” discoveries in the future 🙂


Postscript 1: This reminds me of the OPERA discovery about neutrinos travelling faster than the speed of light – which was found out later to be the result of equipment/calculation errors. Even though in the end this went down not so nicely, at least they right out stated that they were not sure what was going on, and invited everyone to help figure out whether this was a true discovery or an error (In fact, this sparked a lot of good public discussion about particle physics, which was awesome). I gave the OPERA team kudos for that.

Postscript 2: While I am a little sympathetic about the situation ENCODE is in, I don’t have much good to say about ENCODE’s public promo video below. Neither the Human Genome Project, nor ENCODE, is a shortcut to drug discoveries and treatments for rare diseases. They are however critical  steps toward the understanding of how our genome works. It will take a lot more efforts in the future to tease out specifics – and the video seems to convey the message the ENCODE is much closer than Human Genome Project in finding cures for diseases (it isn’t…we don’t even know where the end is…)

Further Reading

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