Monthly Archives: February 2011

Open Laboratory 2011 – submissions so far

Open Laboratory 2011 – submissions so far
The submission form for the 2011 edition of Open Lab is now open. Any blog post written since December 1, 2010 is eligible for submission.

We accept essays, stories, poetry, cartoons/comics, original art.

Once you are done submitting your own posts, you can start looking at the others’, including on aggregators like, and

As I always do, I will keep posting the full list of submitted entries once a week until the deadline – see the listing under the fold.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Help us spread the word by displaying these badges (designed by Doctor Zen:

Continue reading

Web breaks echo-chambers, or, ‘Echo-chamber’ is just a derogatory term for ‘community’ – my remarks at #AAASmtg

As you probably know, I was in D.C. last week, attending the annual AAAS meeting. This was my second one (funny, back when I was a member of AAAS I was still in grad school and I could never afford to go – now that I am out of science, invitations are finally happening). It is an enormous meeting (about 8200 people this year, I hear) and I missed even seeing some of the friends as the space was so enormous and the program so rich.

Unlike last year, when I was in a session that made quite a splash, this year I was a part of a much more academic panel on Social Networks and Sustainability.

Organized by Thomas Dietz of Michigan State University, the panelists were Mrill Ingram (University of Wisconsin), Ken Frank (Michigan State University) and Adam D. Henry (West Virginia University). These are people from areas like sociology, people who make graphs like this one and understand how to properly interpret it:

My role on the panel was as a ‘discussant’, i.e., someone who does not give a separate talk but comments, at the end, on what the other panelists have said.

I am glad I got the materials from the panelists in advance as this was quite dense stuff.

Every scientific discipline invents new words – the terminology (or jargon) with precise meaning that is necessary for practitioners to talk to each other. For the most part, natural sciences tend to stick to agreed definitions, and counter-examples are relatively rare thus usually quite well known (e.g., the different use of the term “gene” by population geneticists vs. molecular geneticists).

Social sciences, on the other hand, tend to appropriate words from the existing English vocabulary and give those words new, precise definitions. Thus, possibility of misunderstanding by non-experts is greater. Also, some of the terms are defined differently by different sub-disciplines, research communities or even individuals, which makes it even harder to be sure one got the meaning correctly.

This all made reading the materials, as well as listening to the panel, quite challenging for me, the outsider in this field. I am also not a researcher of social networks – I am a user and observer, perhaps an amateur student of them. My thoughts could not be supported by numbers and graphs, but had to, by necessity, be more impressionistic – what I learned from my experiences using, living in, and running online social communities.

As all the speakers went substantially over their allotted times all I had left was seven minutes. Fortunately for me, I had all seven (not 3.5) as the other discussant’s flight into D.C. was canceled. Also fortunately for me, this was the very last time-slot of the meeting, so nobody was in a rush to go to another session and thus everyone let me talk a few minutes longer and then remained in the room asking even more questions.

As I tend to do, and in this case particularly, I decided not to prepare too much (OK, at all) in advance. Instead, I listened to the panelists carefully and made the decision what to say only once I climbed onto the podium in the end and knew how much time I had at my disposal. I decided what to say in the first couple of sentences – the rest came out on its own, pure improvisational theater.

As I was reading the materials and listening to the talks, I realized that a couple of examples were clearly discussing real-world, meat-space, offline social networks, but that all the other examples were ambiguous: I could not figure out if those were online, offline, or combined/hybrid social networks.

So, I decided to use my seven minutes to compare and contrast online and offline social networks, how they differ (more important than how they are similar, which is the default thinking), and how they interact and potentially strengthen each other due to such differences.

This is, roughly, what I said – or at least what I meant to say but had to speed up, i.e., this is an (very) expanded version:

Social norms build and enforce echo-chambers

You want to remain in a friendly relationship with the people you see (or potentially can see) often: neighbors, family, colleagues and friends. Nothing makes for a more unpleasant interaction than discussion of politics, ideology or religion with the people you disagree with.

Thus, there is a social norm in place: politics and religion are taboo topics in conversation. It is considered bad manners to start such conversations in polite company.

This means that most people are not exposed to views other than their own in their day-to-day interactions with other people.

In a small tightly-knit community where everyone’s politics and religion are the same (and people tend to move to such places in order to feel comfortable, on top of most likely being born in such a community to begin with), there is no need to discuss these topics as everyone already agrees. If the topic is discussed, there are no other opinions to be heard – it’s just back-slapping and commiserating about the evil enemies out there.

In mixed communities, the taboo against discussing politics and religion is strongly enforced. Again, as a result, there is not much chance to hear differing opinions.

There is no more airtight echo-chamber than a small community which interacts predominantly within itself, and not so much with the outside world.

Mass media builds and enforces echo-chambers

If you are born and raised by parents with a particular set of beliefs, you will also inherit from them the notions of which media outlets are trustworthy. If you were raised in the reality-based community, you are unlikely to waste much time with the media of the fantasy-based community (and vice versa). If your parents read Washington Post, you are unlikely to read Washington Times. You’ll prefer New York Times and not New York Post. MSNBC rather than Fox News. NPR rather than Limbaugh show on the radio.

But it is even worse than that – the choice is really not as broad. The media shapes the public opinion by choosing what is and what is not respectable opinion, i.e., ‘sphere of legitimate debate’ – what opinions to cover as serious, what opinions to denigrate and what opinions to ignore. There are many ideas that people hold that you will never see even mentioned in the US mass media and some of those are actually very legitimate in the Real World.

Furthermore, the press then divides the ‘respectable opinion’ into two opposites, gives voice to each of the two, and will never actually tell you which of the two is more reasonable than the other – “we report, you decide”, aka, He Said She Said journalism.

By presenting every issue as a battle between two extremes (and the fuzzy, undefinable “middle” is reserved only for them, the wise men), the mainstream press makes every opinion something to be sneered at, both those they deem worthy of mentioning and the unmentionable ones.

By refusing to acknowledge the existence of many stands on any issue, by refusing to assign Truth-values to any, by looking down at anyone who holds any opinion that is not their own, the mainstream press fosters the atmosphere of a bipolar world in which enmity rules, and the wagons need to be circled – the atmosphere that is so conducive to formation and defense of echo-chambers and yet so devoid of airing of any alternatives.

The Web breaks echo-chambers

When an individual first goes online, the usual reaction is shock! There are people in the world who believe what!?!?

The usual first response is anger and strenuous attempts at countering all other ideas and pushing one’s own.

But after a while, unbeknown to the person, all those various novel ideas start seeping in. One is not even aware of changing one’s own mind from one year to the next. Many ideas take time to process and digest and may quietly get incorporated into one’s gradually enriching and more sophisticated worldview.

We all learn from encountering all those other opinions even if we vehemently disagree with them. And we cannot help bumping into them all the time. There are no taboo topics online, no social norms preventing people from saying exactly what they think.

Forming, finding or defending a vacuum-sealed echo-chamber online is extremely difficult, if at all possible.

Your Facebook friends will post stuff that reveals their politics is different than yours (and you did not even know that about them before – they seemed so nice in real life!). By the time you get around to blocking them…it’s too late – the virus has already entered your head [this one sentence added 2-27-11].

People you follow on Twitter because of some common interest (e.g., food or knitting or parenting or technology or geographic area) may be very different from you when concerning some other interest, e.g., religion, and will occasionally post links to articles that contain opinions you have never heard of before.

If you are, for example, a liberal and tend to read only liberal blogs, you will constantly see links to conservative sites that are being debunked by your favourite bloggers – thus you will be exposed to conservative ideas daily.

If your interest is science, you are even luckier. The mainstream media, if it links to anything at all, tends to link either to each other or to governmental sources (e.g., CDC, USDA, etc.). Political bloggers link a lot more, but again the spectrum of sources is pretty narrow – they link to MSM, to governmental pages, and to each other (including the “opposition” bloggers).

But science bloggers link to a vastly broader gamut of sources. If mass media is linked to at all, it is usually in order to show how bad the coverage was of a science story. Linking to each other is important (and that includes linking to anti-science sites when needed to counter them), but what science bloggers do that others do not is link to scientific papers, documents, databases, even raw data-sets (including some Open Notebook Science bloggers who pipe data straight from their lab equipment onto the web).

What echo-chamber? Contrary to what some uninformed op-eds in the mass media like to say, the Web breaks echo-chambers that the social norms and mass media have previously built.

The online and offline social networks can work synergistically to affect real change

Many curmudgeons like to say that the Web does not do anything on its own. They (unlike behavioral biologists) do not understand the distinction between Proximal Causes and Ultimate Causes. Web is a tool that allows, among other things, many more people in much shorter time to organize to do something useful in the real world.

Release of Tripoli 6 was an instance in which massive outpouring of support online forced the mainstream media to cover the story which then forced the hand of politicians to do something.

Likewise, in the case of resignation of George Deutsch from NASA, it was investigative work by a blogger, Nick Anthis, that energized the blogosphere, which pushed the MSM to finally report on the story, which forced the event to happen.

PRISM was an astroturf website built to counter the pro-open-access NIH bill in the US Senate. Outpouring of online anger at the tactics by the publishers’ lobby inundated the senatorial offices – as a result the bill passed not once, but twice (GW Bush vetoed the first version of the large omnibus bill it was a part of, then signed it with no changes in the language on this particular issue) and the Senate is now educated on this issue.

But probably the best example is the Dover Trial (Kitzmiller v. Dover Area School District) that made Intelligent Design illegal to teach in US public schools. The ruling by Judge Jones (pdf) is one of the most powerful texts in the history of judicial decisions I am aware of.

There are anti-evolution bills popping up somewhere in the country seemingly every week. But because of the Dover ruling, they are all illegal. Most don’t make it to the committee, let alone to the floor of the state legislatures. Others are soundly defeated.

Before Dover, both Creationist sites and pro-evolution sites, when linking to me, would bring approximately the same amount of traffic to my blog. After Dover, getting a link from PZ Myers, Richard Dawkins, Larry Moran or Jerry Coyne brings substantial new traffic. Links from Creationist sites? Essentially undetectable by traffic trackers – I discover them only when I search my blog URL to specifically see if there are new links out there. Creationism, while still popular with the people, is politically essentially dead. The Dover ruling castrated it.

But Dover Trial would not have gone that way, and would not result in such a gorgeously written document by the Judge, if it was not for a small army of bloggers who contribute to the blog Panda’s Thumb. A mix of scientists from different disciplines, lawyers, etc., this group has been online – first on Usenet, later on the blog – for a couple of decades before the trial.

This is a group of people who battled Creationists for many years, online and offline, in courtrooms and political campaigns, in classrooms and in print. They know all the characters, all the usual creationist “arguments” (and provided all the answers to them in one place), all the literature, etc.

It is one of them who discovered that the new Intelligent Design “textbook” is really just a reprint of an old Creationist book, in which the word “Creationists” was replaced by “Intelligent Design proponents” throughout the text….except in one place where they made a typo: “Cdesign proponentsists”.

Ooops – a huge piece of evidence that Intelligent Design Creationism is just a warmed-up version of the old-style Creationism masquerading as something new. The Panda’s Thumb bloggers were at the trial as expert witnesses who provided all the expert evidence that Judge Jones needed to make his decision. People who organized on the Web have helped a meatspace history come to pass.

The online and offline social networks can work synergistically if the ecology is right

When looking at the role of online communities and networks in meatspace events, counting the numbers of networked citizens (or ratio of networked to non-networked citizens) is not sufficient – one also needs to know their geographic distribution, and their connectiveness with non-networked citizens. The most fresh example are the so-called “Twitter revolutions” in the Arab world.

There are at least two possible scenarios (or thought experiments) that demonstrate the importance of ecological thinking about social networks:

1) There are 10 people on Twitter in a country. All in the same city, all in the same college dorm, good friends with each other. No communication with other people. No Twitterati in other cities. Nobody knows that other people in other cities have the same negative feelings toward the government.

2) There are 10 people on Twitter in a country. One each in 10 different cities. They communicate with each other via social networks continuously. Each is also a center of the local community of thousands of non-networked people using offline methods of communication. Through this connection, they become aware that there are millions of them, all over the country, and that a revolution is feasible.

In scenario 1, there are 10 buddies dreaming of revolution. In scenario 2, there are thousands of people in ten cities organizing revolution. In both, there are only 10 people on Twitter. Yet, the outcome is likely to be very different.

Thus, the ecology of the networkers, their spatial and temporal distribution, and their effectiveness in informing not just each other but many non-networked citizens, are important data one needs for this exercise.

‘Echo-chamber’ is just a derogatory term for ‘community’

I shamelessly stole this sub-heading from someone on Twitter (let me know who said it first if you know). Edit: Thank you – it was Chris Rowan,

A great example of a case where the Web produced a community (aka echo-chamber) but that was a good thing, is the case of American atheists.

Before the Web, each atheist in the USA thought he or she was the only one in the country. The social norms about the impoliteness of discussing religion, as well as the real fear of reprisals by the religious neighbors, made atheism completely invisible. No need to mention that the media never mentioned them – they were outside of the “sphere of legitimate debate”.

But then the Web happened, and people, often pseudonymously, revealed their religious doubts online. Suddenly they realized they are not alone – there are millions of atheists in the country, each closeted before, each openly so after! It is not a surprise that “no belief” is the fastest-growing self-description in questions about religion in various nation-wide polls and censuses.

President Bush Senior, himself not very religious, could say that atheists are not real American citizens. A decade later, his son GW Bush, himself a fundamentalist, could not say that any more – his speechwriters made sure he mentioned atheists in the listings of all the equally American religious groupings.

Not all online communities need to be politically active. Discovering people with the same interest in knitting is nice. Exchanging LOLcat pictures is fun. But such interactions also build ties that can be used for action in the real world if the need arises.

Without the Web, I would not know many people whose friendship I cherish. Without the Web I would not have this job. Without the Web, me and many of my friends would have never gone to a meeting like AAAS. There would be no such meetings as ScienceOnline, Science Online London, SciBarCamp, SciFoo, and others.

Every time I travel I make sure that people I know online – from blogs, Twitter, Facebook etc. – know I am traveling. I say on which date, at which time, I will be in which restaurant in which city. Twenty people show up. Most I have never met in real life before. But after sharing a meal, a beer, a handshake and a hug, our weak ties become strong ties. Superficial relationships become friendships. If there is a need to organize some real-world action – we can rely on each other to participate or help.

I have a separate Dunbar Number in each city I visited. And I try to connect them to each other even more than they are already connected via online communication. Which is one of the reasons we organize conferences and one of the reasons I am online all the time.


As Science Bloggers, Who Are We Really Writing For? by Emily Anthes.

Are science blogs stuck in an echo chamber? Chamber? Chamber? by Ed Yong.

Two new posts on the SciAm Guest Blog

Again today, we have two new posts on the Scientific American Guest Blog.

First, Reflections on biology and motherhood: Where does Homo sapiens fit in? a wonderful post by Carin Bondar.

Then, Colin Schultz covers a study with a provocative finding (especially for Web curmudgeons) – You’ll believe anything you read online, won’t you?

As always, read, enjoy, comment, share…

Two new posts on the SciAm Guest Blog – stonefaced justices, and frozen stoneflies

There are two new posts on the Scientific American Guest Blog today.

First one in the morning is the post by Seth Mnookin, responding to yesterday’s Supreme Court decision in the Bruesewitz v. Wyeth case, and especially the Sotomayor dissenting opinion, in The impossibility of responsible nuance in the vaccine discussion

Then at noon, Holly Menninger explained how cold-tolerant insects survive winters, in Winter stoneflies sure are supercool.

Read, comment, share…

Introducing ‘Anecdotes from the Archive’ – a new Scientific American blog by Mary Karmelek

Today we added the eight blog to the current roster of Scientific American blogs (no, that’s not the network yet) – Anecdotes from the Archive.

You have seen a few of the posts already on the Guest Blog. They have now been moved to the new blog, where Mary Karmelek will bring you joy roughly twice a week. From the About page:

In 1845 Scientific American magazine made its debut on newsstands and has continued to be published ever since. Now, Nature Publishing Group and Scientific American are working to digitize all past issues of the magazine. Mary Karmelek is in charge of checking over each issue, and in the process she uncovers fascinating, captivating and humorous material buried in the yellowed pages of our past. In this blog she shares the highlights of her discoveries. Additional archival material appears every month in our 50, 100 and 150 Years Ago column.

New post on the SciAm Guest Blog – on ‘manufactoversies’

Today on the Scientific American Guest Blog, a new post is a book review by Dr. Val, on ‘manufactoversies’ and how the moneyed interests saw the seeds of denialism – Review: How the Internet is being used to hijack medical science for fear and profit. Emjoy, comment, share…

Two new posts on the SciAm Guest Blog

Just got home, after a day on the train. But Guest Blog was not sitting idle. There are two new posts today.

First, Mary Karmelek asks: What’s black and white and brown all over?

Then, in Heart interrupted, Jeanne Garbarino explains what a heart-attack is and how to deal with it.

Read, comment, share…

New post on the SciAm Guest Blog

Done with the AAAS meeting, did my panel this morning, finally getting back online, traveling home tomorrow.

But there is a new post on the Scientific American Guest Blog anyway (viva scheduled posting).

So, go over there and read Ecological opportunity: The seed of evolutionary change in your backyard–and in your veins by Jeremy Yoder….enjoy, comment, share.

Open Laboratory 2011 – submissions so far

The submission form for the 2011 edition of Open Lab is now open. Any blog post written since December 1, 2010 is eligible for submission.

We accept essays, stories, poetry, cartoons/comics, original art.

Once you are done submitting your own posts, you can start looking at the others’, including on aggregators like, and

As I always do, I will keep posting the full list of submitted entries once a week until the deadline – see the listing under the fold.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Help us spread the word by displaying these badges (designed by Doctor Zen:

Continue reading

Three new posts on the SciAm Guest Blog

I am at the AAAS meeting in D.C. so not online much. But the Scientific American Guest Blog is running along just fine.

Two posts yesterday and one post today:

First, yesterday morning, Ugly animals need love, too by David Manly.

Then, yesterday afternon, Anecdotes from the Archive: Map Making on Wheels by Mary Karmelek.

Finally, earlier today, Life 2.0? First let’s figure out Life 1.0 by Alaina G. Levine.

As always, read, comment, share…

Two new posts on the SciAm Guest Blog

Two new posts on the Scientific American Guest Blog this morning.

First, Pleasure, reward…and rabbits! Why do animals behave as they do? by Michael Lisieski.

Then, ,Climate research in the geologic past by David Bressan.

Read, comment, share….

Two new posts on the SciAm Guest Blog – Sundance films, and MRI-safe pacemakers

Again today, two posts on the Scientific American Guest Blog.

First, Tamara Krinsky continues with her reporting from the Sundance film festival, focusing this time on “Another Earth”, in The Sundance Diaries: Focus on the Alfred P. Sloan Foundation.

Then, a piece of serious investigative journalism that is informative, useful and important – New wave of MRI-safe pacemakers set to ship to hospitals by Mary Knudson.

As always, read, enjoy, comment and share…

ScienceOnline2011 (and ’10, ’09, ’08, ’07) reunion at AAAS meeting this Friday night!

If you have ever attended any of our ScienceOnline conference in the past, and you will be in Washington DC this week, probably to attend AAAS meeting, please join us for a little reunion on Friday at 9pm at La Tasca Tapas and Bar, 722 7th St. NW (click on the image above to see bigger):

Two new posts on the SciAm Guest Blog

Today we again have two posts on the Scientific American Guest Blog.

First, You are what you bleed: In Japan and other east Asian countries, some believe blood type dictates personality is fascinating, by Rachel Nuwer.

Then, Anecdotes from the Archive: Happy 95th anniversary to….Electrical Prosperity Week! byMary Karmelek in her bi-weekly dig through the SciAm 165-year long archives.

Two new posts on the SciAm Guest Blog

There are two great (longform) new posts on the Scientific American Guest Blog today.

First, Doctor, what’s wrong with my child?–what Guido Fanconi taught us about chemotherapy by The Genomic Repairman.

Then, a Valentine’s Day special – Of lice and men: An itchy history by Emily Willingham.

As always: read, enjoy, comment, share….

Open Laboratory 2011 – submissions so far

Open Laboratory 2011 – submissions so far
The submission form for the 2011 edition of Open Lab is now open. Any blog post written since December 1, 2010 is eligible for submission.

We accept essays, stories, poetry, cartoons/comics, original art.

Once you are done submitting your own posts, you can start looking at the others’, including on aggregators like, and

As I always do, I will keep posting the full list of submitted entries once a week until the deadline – see the listing under the fold.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Help us spread the word by displaying these badges (designed by Doctor Zen:
Continue reading

Darwin Day at Scientific American

Sorry, I’m late posting this – but earlier today we had a post on the Scientific American Guest Blog on the occasion of Darwin Day.

Written by the perfect person for the occasion, Karen James, the post Evolution isn’t easy, even in Galapagos is beautiful and thought-provoking. Read it. Then comment and share.

My new science post on the SciAm Observations blog – History of circadian genetics research

I wanted to write about this for years. Finally a good opportunity emerged: two new circadian papers provided the “news hook” for a blog post I wanted to write providing historical, philosophical, sociological, theoretical and methodological context for the findings in circadian genetics.

I also used the new tool – Dipity – to make timelines of key events in this history. The post is long, but serves as an Explainer, a “basics” post and a source of important references, so I hope people bookmark it for future reference.

I hope you have the time and patience to read it (perhaps save on Instapaper and read on your daily train commute):

Circadian clock without DNA–History and the power of metaphor

Then let me know what you think – comment there, share the link on social networking sites, respond on your own blogs, etc….

Circadian clock without DNA–History and the power of metaphor Last week, two intriguing and excellent articles appeared in the journal Nature, demonstrating that the transcription and translation of genes, or even the presence of DNA in the cell, are not necessary for the daily (“circadian”) rhythms to occur (O’Neill & Reddy 2011, O’Neill et al., 2011). (Scientific American is part of Nature Publishing Group.)

The two papers received quite a lot of media coverage, and deservedly so, but very few science bloggers attempted to write in-depth blog posts about them, placing them in a broader historical, theoretical and methodological context. I had a feeling that everyone was waiting for me to do so. Which is why you are now reading this. I know it is a long “Explainer” (which is all the rage in science journalism these days) but I hope you have patience for it and that you find it informative and rewarding.

What I intend to do is to, first, briefly describe and explain the research in these two papers, though the press release and media coverage were quite accurate this time. Diana Gitig did the best job of it at Ars Technica – I highly recommend you read her piece for clear background information.

Then I will try to give you a historical perspective so you can get a feel for the context in which this research was performed. This look at the history will bring into sharp relief how powerful the scientific metaphors are in guiding the questions that researchers try to answer in their laboratories. Finally, a look at the media coverage will show that the lay audience (including journalists) is guided by other metaphors – not always the same ones that are used by researchers.

What did they do?

In each of the two papers, the researchers chose an unusual laboratory model for their study. What is common to both models is that a) they are both Eukaryotic cells and b) there is no DNA transcription or RNA translation going on inside the cells.

In the first study (O’Neill & Reddy 2011), they used human red blood cells (photo left) as these cells have no nucleus, thus no DNA at all.

In the second study (O’Neill et al. 2011), the model of choice was a small protist, Ostreococcus tauri which has an interesting property – when kept in constant darkness, there is no DNA transcription or RNA translation that can be detected.

The starting point of both studies was detection of peroxiredoxins in the cytoplasm. Peroxiredoxins are enzymes (thus chemically proteins) that protect the cells from damage from strongly oxidizing molecules (often refered to as “free radicals”). The process of neutralizing such oxidants temporarily changes the chemical structure of the peroxiredoxin, which then reverts to its native state again – thus the molecule is constantly switching between the two states. This oscillation between the two states follows a daily (~24h) cycle synchronized to the day-night cycle of the environment.

In both studies, peroxiredoxins were detected using antibodies (“immunoblotting”). One of the chemical states of the molecule can be detected with this method, while the other state is indirectly detected by the comparative lack of signal. Thus a circadian rhythm would be seen as an alternating series of rises and falls of the detected signal with a period close to 24 hours.

And this is exactly what they discovered in both cases – there was a clear circadian rhythm of peroxiredoxins state-switching both in cultured red blood cells (above right) and in the cultured Ostreococcus tauri (below).

Furthermore, in the protist study, they used measurement of light emitted by luciferase added to the sea-water solution as a marker of DNA transcription and translation. While the cells were kept in constant darkness no light emitted due to presence of luciferase could be detected.

But at the onset of environmental light, luciferase-induced light measurements indicated that the transcription started at the phase predicted from the state of the clock before the cells were placed in the dark. This means that the circadian rhythm of DNA transcription did not start at some “Phase Zero,” triggered by switching on the light, but that it was driven by a clock that was operating all along while the organism was kept in the dark – a clock that does not require DNA transcription and translation.

Detecting a 24-hour rhythm is not sufficient to ensure that the rhythm is actually circadian. For a biological cycle to be considered circadian, it has to satisfy a number of criteria, e.g., it has to be endogeonous (generated inside the cell, not forced onto it by the environment), it has to persist for several cycles, it has to be unaffected by temperature levels (i.e., the period of the rhythm should be the same regardless of the level of environmental temperature kept constant in the laboratory), it has to be entrainable (synchronizable) by imposed cycles in the environment, etc.

In both model systems, the researchers performed (either in these or prior studies) the entire battery of standard experimental protocols to demonstrate that yes, these are indeed circadian rhythms in both laboratory models.

Use of temperature cycles instead of light-dark cycles to demosntrate entrainment in the first experiment makes sense as human red blood cells do not experience (and cannot detect) light, while they are normally exposed to daily fluctuations of body temperature. The difference between the dawn minimum and evening maximum temperature inside the human body can be as large as 1 degree Celsius, more than sufficient for entrainment – some entire cold-blooded animals like lizards, insulated from the environment by skin and scales, can entrain their rhythms to temperature cycles with the high-low difference as small as 2 degrees Celsius and in some individuals as small as 0.1 degrees (Underwood and Calaban 1987).

In the red blood cell paper, the researchers went further. They also detected circadian rhythms in a few other biochemical processes. For example, hemoglobin, the molecule that transports oxygen from the lungs to the cells, and carbon dioxide from the cells to the lungs, can exist in two different forms inside red blood cells. It is a complex protein molecule, built of four almost-identical units. In this form, hemoglobin can perform its normal function. But there is also a two-unit form which cannot perform the function in gas exchange. Furthermore, the two-unit form produces the oxidizing small molecules – exactly the kinds of molecules that peroxiredoxins have evolved to scavenge and neutralize. It is not surprising that the switching between two-unit and four-unit forms of hemoglobin was also seen to be circadian – and in sync with the peroxiredoxin rhythm.

Likewise in the protist paper (see O.tauri in the photo at right), the researchers performed a whole suite of additional experiments designed to eliminate a variety of potential alternative hypotheses. For example, pharmacological suppression of DNA transcription and translation did not eliminate the circadian rhythm in peroxiredoxin chemistry, but instead demonstrated a complex interplay between the clock driven by transcription of genes and the clock driven by spontaneous biochemical reactions in the cytoplasm.

In summary, the two papers are very solid, the experiments are well designed and performed, the results are persuasive, and the names of authors give me confidence that the data can be trusted.

What does this all mean?

The results of both papers demonstrated that transcription of DNA and translation of RNA is not necessary for the generation of circadian rhythms in two different types of eukaryotic cells belonging to evolutionarily very distant relatives – protists and mammals.

In the case of red blood cells, the result is clear – there is no DNA or RNA in these cells. Thus, the circadian rhythms in these cells have to be generated in the cytoplasm.

In the case of O.tauri, the picture is a little bit more complex: the cells have a nucleus which has DNA. There is a clock driven by transcription and translation of canonical “clock genes.” Yet, when this mechanism is supressed – either by constant darkness or by chemicals – the cells still exhibit circadian rhythms generated by the molecules residing in the cytoplasm (and some of those molecules, at least during the first day or two, may be strands of RNA transcribed earlier).

Furthermore, the phase at which the DNA-centered clock starts its cycle is determined by the phase of the cytoplasmic clock, not the other way round, i.e., the cytoplasmic clock is dominant over the nuclear clock.

Why is this so exciting?

Depends who you ask!

When the articles were first published I did not yet have time to read them carefully. But I have e-mail notifications set up so every time Google detects a news article or blog post containing the word “circadian” I get a message. Thus I read a number of media articles about these studies before I read the studies themselves.

The media accounts (see some examples) tended to emphasize two reasons why these studies are important.

The first one was a surprise that both humans and protists have the same molecules doing the same thing. Their surprise was a surprise to me! Circadian clocks are found everywhere. Peroxiredoxins are found in almost all living organisms on Earth. Just like the structure of cell membrane, the processes of DNA transcription and RNA translation, the genetic code, or the use of ATP (adenosine triphosphate) as the energy currency of the cell, peroxiredoxins are ubiqutous molecules in almost all of life on this planet.

Those are life’s universals, something that is expected as we have understood the unity of life even before Darwin. These universals are, to a biologist, usually deemed pretty useless and boring – the background. What gets a biologist excited is variation – the exceptions to the universals. If most organisms use a particular molecule for a particular function but one organism does not – now that is exciting! Why is this? How and why did this organism evolve this switch in function? What was the initial mutation, what was the selective pressure? Those are useful questions in biology that help us understand evolution.

My hunch is that the journalists, either by being lay audience themselves or by targeting their articles to the lay audience as they understand it, focus on the universals – the “Unity Of Life” – as something that in their minds is evidence for evolution and a counter-argument against non-scientific ideas about life (e.g. intelligent design creationism). While biologists find surprise and delight in exceptions, which are useful entries into detailed studies of evolutionary mechanisms, many in the lay audience are still surprised by the plain fact of the unity of life as it evolved from a single common ancestor.

The second reason given in MSM (mainstream media) articles as to why these studies are important is their novelty. For example, Chemical & Engineering News states that this “…involves a previously unknown cycle of posttranslational modifications, in addition to the transcription of a well-known handful of clock genes…”

There is a sense, reading all the coverage, that this is so novel, creative and revolutionary, it must have been the very first time anyone has ever thought of this! And even better – this is a great “conflict” story, in which a single study puts into question an entire field! A small group of young geniuses proved the entire old establishment wrong!

Not so fast!

Both of these studies have been done before. Several times.

I quickly went to the PDFs of the two papers and yes, the references to the old studies are there. The authors are aware of the history of the field, the giants on whose shoulders they climbed in order to see further. Of course, these are Nature papers with severe constraints on space and on the number of references. With so many experiments and so much to explain about their methods and results, they could not spend enough time on the history of the idea and on the work of their predecessors. And they could not cite all of the preceeding studies. But they chose the key ones and noted them briefly in the text – not prominently, but they are there.

So why did the MSM articles not pick up on this? First, by stressing the novelty – and the “conflict” story of geniuses proving the establishment wrong – they make the new studies seem more newsworthy, thus more likely to be approved by the editors to get into print.

Second, the MSM articles are limited by space and there is only so much one can put in 500 words. Thus, as usual, it is the context that gets left out and the novelty-factor that remains in the piece.

Finally, even if a dilligent journalist wanted to follow up on the background he or she would bump into the dreaded paywalls.

Nobody expects a journalist to know as much about the field as its practitioners do. I knew exactly what to look for and even I needed a few days to collect all the papers and read them – which is why you are reading this post now instead of last week.

As a member of the Society for Research on Biological Rhythms I have free access to the Journal of Biological Rhythms, the premier journal in the field. Once logged in, I knew exactly which five articles to look for. Those five articles (all cited below) contained the references to all the other papers I was interested in. As none of those are Open Access, I had to go to Twitter and, by using the hashtag #ICanHazPDF ask my followers to find me and send me PDFs of all of these papers. I got most of them (though some are not available or not even digitized yet as many of them are quite old). Then I had to spend some time reading them.

This all takes time, and I had the advantage of knowing where to start…perhaps even the advantage of being aware, to begin with, that such studies exist. Even Allison Brager who is in the field of chronobiology, did not note on her blog Dormivigilia the existence of prior research and exclaimed with excitement that “….the clinical and scientific relevance of this work are HUGE!!!!….” It is not always stressed hard enough to graduate students how important it is to read the historical literature of one’s field.

So, let’s quickly go through some of the aspects of the history of circadian research that are most relevant to the understanding of the context in which these two papers appeared.

Brief history of clock research

While the observations of daily rhythms in plants and animals go back to the antiquity, the first experiment in the field was performed in 1729 by Jean-Jacques d’Ortous de Mairan who observed the rise and fall of leaves of a Mimosa plant kept in constant darkness. Much early research was done in the 19th century, mostly on plants, but also a little bit on insects and humans.

In the early 20th century a number of people started studying rhythmic phenomena in living organisms. They came from very different scientific disciplines, e.g., botany (Bunning), ecology (DeCoursey), animal behavior (Kramer, Beling, Sauer), protozoology (Hastings), evolutionary biology (Pittendrigh), mammalian physiology (Richter), human biology and medicine (Aschoff, Halberg), and agriculture (Garner and Allard). It took them a few decades to discover each other’s work and to recognize that they are dealing with the same phenomenon regardless of the organism they were studying, be it fiddler crabs, starlings, tobacco or humans.

The founding moment of the field was the 1960 meeting at Cold Spring Harbor. The book of Proceedings from the Meeting (Symposia on Quantitative Biology, Vol.XXV) is a founding document of the field: I own three copies, strategically placed in three different spots in the house so at least one copy has a chance to be saved in case of fire. And you can bet I have read it over and over again during my 10 years in grad school (and after).

In 1960, structure of DNA was very new, and comparatively little was known about the inner workings of a cell. But most researchers were eager to break into the ‘black box’ and start investigating how the circadian clock ticks inside of the cells. A number of conceptual models were proposed, some focusing on cell membranes, others on DNA. Thus, experiments were started to separate the two parts of the cell and to test the role of nucleus and DNA in the clock mechanism.

Roenneberg and Merrow (2005) provide an excellent timeline of the research since then, especially the emergence of molecular and genetic techniques and subsequent findings. But briefly, over the next two decades or so, circadian mutants were discovered in a protist (Chlamidomonas), insect (Drosophila) and mammal (Golden hamster). The first canonical clock gene – the Drosophila period gene – was sequenced shrtly after.

Around 1995, clock genetics explodes. New clock genes were discovered left and right in several different organisms, from cyanobacteria to humans. There was a sudden influx of people into the field from other areas of genetics, and they required a few years to catch up on the field’s history and theory before they stopped making beginners’s mistakes in their experimental designs (though see Dunlap 2008 for different perspective on that history). But there were many of them, they had plenty of funding, they were excited and creative, had powerful new techniques, and they worked fast, so every week, or so it seemed at the time, there was a new discovery of genes involved in circadian rhytms.

Here is a timeline of the key events in this aspect of the history of the field:

What emerged from all of this activity is the transcription/translation model (Hardin, Hall & Rosbash 1990) for the circadian mechanism: a suite of canonical clock genes get transcribed and translated, and their protein products, after some delay, inhibit the transcription and translation of those same genes. Day in and day out. Those genes and their products then also regulate expression of all the other genes that the cell uses in its daily function.

But not all were happy with it.

If you read Dunlap 2008 you will certainly detect a tension between researchers who studied whole organisms (always with evolution in the backs of their minds) and treated the clock as a ‘black box’ for decades before the genetic explosion, and the geneticists who came into the field in the mid-1990s. The former regarded the latter as arrogant and simplistic in their complete focus on DNA. The latter regarded the former as out-dated holists who don’t understand the magnificient power of DNA and treated them like Lysenko by those who do not understand Lysenko.

You need to remember that this was in the middle of the Human Genome Project hype, when there was a huge overselling of crude genocentric and gene-deterministic ideas, many of which were fully embraced by the geneticists at the time (they have learned better since then).

I do not want to exaggerate the tension – it was mostly muted. Geneticists were mainly welcome into the field. After all, they were bringing in their tools and skills to do what the field was hoping to do all along – crack open the “black box” and peer inside. The two groups treated each other with respect, and soon started collaborating. The old guard of chronobiology was impressed by the speed and capability of the genetics labs, the rate at which new techniques were developed and improved, and the rapidity of discoveries. They learned (or sent their students to learn) the techniques, and started thinking how to employ them to study circadian phenomena that prior research has already shown occured at higher levels of organization.

The hope was that the genetics and molecular approaches will quickly discover all the core clock genes and the way they interract with each other so the focus can shift back to explaining the things that really matter – properties of ensembles of clock cells and the behaviors of whole organisms (after all, DNA is invisible to selection – phenotype of the whole organism is what ecology and evolution can see to act upon).

The discovery of clock genes required the use of a limited number of laboratory models that are amenable to genetic dissection: mouse as the model for all vertebrates, fruitfly representing all invertebrates, Neurospora crassa standing in for all fungi, Arabidopsis being “the plant” and Synechococcus being used as the only bacteirum known (at the time) to possess a circadian clock. In the early years, a few protists were also used – Paramecium, Euglena, Gonyalax, Acetabularia and Chlamydomonas, but they were later largely abandoned, while new models, like Xenopus and zebrafish entered the arena.

This was a highly unusual state for the field – chronobiology was always extremely comparative, with thousands of species of organisms being studied over the years. The hope was that, once the genes are discovered in model organisms, the findings can be applied to other creatures for a more comprehensive and comparative research program.

Likewise, the focus on genes was also seen as temporary, something to be “waited out” until the findings can be applied to other levels of organization in a more integrative approach. Thus, entire lines of research were reduced or have essentially stopped – tidal, lunar and circannual rhythms, Sun-compass orientation, photoperiodism, development, ecology and evolution – waiting for new techniques and new findings that will enable them to re-start.

And that is exactly what happened – a decade or so later, the field concluded that all the core clock genes were discovered and that the transcription/translation feedback loop model is good enough. The study of previously semi-abandoned topics (and organisms) started with new zeal and gusto.

Persisting problems

At the time of the Cold Spring Harbor symposium in 1960, there were two main lines of thinking about the cellular mechanism of the circadian clock. One focused on the nucleus and the DNA (Ehret and Trucco 1966). The other focused on the cell membrane (Njus et al. 1974).

How does one go about figuring out which one of the two models is right, using techniques available at the time?

One approach is to use cells that do not normally possess a nucleus or any DNA – like mammalian red blood cells – to see if they have circadian rhythms. If yes – nuclues is not important, membrane (or cytoplasm) is. Studies were difficult and results not always clear, but most could detect rhythms in red blood cells (Cornelius and Rensing 1976, Mabood et al. 1978, Ohm-Schradera et al. 1980, Peleg et al. 1990a,b)

Second approach is to use very large cells that can survive long enough once the nucleus is removed – in comes the protist Acetabularia (Sweeney and Haxo 1961, Schweiger et al. 1964, Vanden Driesche 1966,Terborgh and McLeod 1967, Vanden Driesche and Bonotto 1969, Sweeney 1974, Mergenhagen and Schweiger 1975a,b, Hartwig et al. 1985, Woolum 1991, Runft, Linda and Mandoli 1996). These studies showed that clock operates after the nucleus is removed, and, once the nucleus is reintroduced, it is the clock in the cytoplasm that determines the phase, entraining the nuclear clock.

The third approach is to pharmacologically block DNA transcription and RNA translation. This was, over the years, performed in a number of organisms, including Acetabularia (photo on the right) and, much more recently, the sea-slug Bulla gouldiana (Page 2000). Again, rhythms persisted in the absence of DNA transcription.

Fourth approach is to find single-cell organisms that reproduce or divide more often than once a day and see if the circadian phase is preserved during the process – there is no DNA transcription during cell division. This was initially done in the protist Paramecium (Barnett 1966), but later it was cyanobacteria that were used in this approach (Mori et al. 1996, Kondo et al. 1997). Circadian phase is preserved during reproduction in Paramecium and cell-division in bacteria.

Fifth approach is to find organisms that have circadian rhythms but do not have clock genes. Yeast (Saccharomyces cerevisiae) is one such organism. In the nematode Caenorhabditis elegans, which shows circadian rhythms, the genes usually used for circadian timing are instead used for developmental timing (so-called heterochronic genes).

Sixth approach is to study the rhythms in either the cell membranes (for example in the protist Gonyalax polyedra, Adamich et al. 1976, or fruiftly, Nitabach et al. 2005) or elements of the cytoplasm directly, in a dish (using bacterial clock proteins, Tomita et al. 2004, Mehra et al. 2006, Mori et al, 2007). Again, the isolated cell membrane cycles, and blocking the membrane processes also blocks overt rhythms in whole organisms. Bacterial clock proteins (not DNA) kaiA, kaiB and kaiC, when placed in a test tube, spontaneously oscillate in a circadian fashion.

Finally, one can genetically affect the clock: mutating, deleting, shutting down or overexpressing (forcing expression at high levels at all times with no cycling) canonical clock genes and see if any residual rhytmicity remains. This was done in the fruitfly (Helfrich-Förster 2000), where morning peak of activity is eliminated when the clock gene cycling is stopped, but the evening bout of activity in male flies persists nonetheless. Sometimes a genetics paper would triumphantly state that a deletion of a gene rendered half of the flies arrhythmic, just to be met with a question “so, how do the other half of the flies still cycle without it?”

This research program started with enthusiasm immediatelly after the symposium, yielding troves of interesting data over the years. But, once the geneticists entered the fray, these results were forgotten or ignored. They did not conform to the DNA-based model. The easiest way to make a circadian geneticist in the mid-1990s angry at a conference was to utter the word “Acetabularia” – this was “noise” to be ignored and swept under the rug.

You can see the timeline of the history of this “shadow research program” here:

Why did this research persist despite the victorious run of the transcription/translation model?

The earliest studies in this area were a direct outgrowth of the ideas discussed at Cold Spring Harbor. They all yielded the data suggesting that DNA is not the only part of the clock mechanism. Yet, once genetics work took off, these results were ignored. At least some of the people in the field were worried that genetic work is ignoring something potentially important.

Who in the field was worried about this depended on their own background and experience? First, people who worked on organisms that yielded unusual experimental data throughout the history of circadian research, including the fungi and the protists (especially Gonyaulax polyedra, recently renamed Lingulodinium polyedrum but you are unlikely to find many circadian papers using the new name, and the systematics may still be in flux) were one such group.

People working on non-mammalian vertebrates (fish, amphibians, reptiles and birds) were cognisant of the complexity of circadian organization – same clock genes, expressed in different tissues, resulted in clocks of different properties. The clock in the pineal organ, the clock in the retina, the clock in the SCN (suprachiasmatic nucleus of the hypothalamus), the peripheral clocks in all the other tissues – each of those behaved differently despite using the exact same molecular machinery. So the properties must have been modified by something else in the cell, or by the interactions between cells in the tissue.

On top of that, many phenomena, e.g., photoperiodism or sleep, are not properties of individual cells but of interactions between ensembles of cells in the tissues, or even interactions between the organism and its environment. The simplistic “this gene is for clocks” model just could not explain the complexity of observed reality.

Once all the clock genes were deemed discovered, the critiques started popping up (Roenneberg and Merrow 1998, 1999, 2005, Lakin-Thomas 2000, 2006), trying to move the circadian research up the levels of organization to the interplay between cells, tissues, organs and organisms. Most of these calls for the return to the organism were reviews of all the studies showing that DNA is not enough – somewhat like this article is. The two Nature articles last week are just the latest research results in this tradition.

The power of metaphor

Where does this fundamental misunderstanding between molecular and organismal biologists come from? They are both biologists, right? So they should be expected to operate from the same basic principles.

But they don’t. Geneticists come from a tradition starting with Schroedinger’s 1944 book What is Life? This is a linear, hierarchical view of life, with upward causation: genes cause and control everything else. Also, gene is the only level on which natural selection acts (Dawkins 1976). The reigning metaphor of this worldview is the “program.”

On the other hand, biologists coming from the study of evolution, ecology and animal behavior have a “systems” view of life in which many interacting elements, none of them with a primacy, determine the behavior of the entire system. There is no single element in control. The phenomena are a result of interactions, not of dominance of any particular actor.

The causation is downward (natural selection). DNA is just one of the elements in the system. Selection acts simultanously at several levels, including whole organisms and groups (Brandon 1996, Gannett 1976, Godfrey-Smith 1999, Griffiths and Gray 1994, Hubbard and Wald 1993, Keller 1995, Lewontin 1992, Nijhout 1990, Nelkin and Lindee 2004, Kitcher, P. 1999, Rose et al. 1990, are just a tip of the iceberg of the literature analyzing and criticizing the hierarchical DNA-first worldview). The reigning metaphor of this worldview is “the tangled bank”.

Circadian field is not the only area of biology in which these two worldviews clashed. But it is worth noting here that the studies of clock genes ignored everything else, while the studies that questioned DNA supremacy never just shifted the control to some other element – all of those studies say that DNA is not sufficient, not that it is replaced by another controller.

Let’s look at the “program” as a metaphor. A program is a term from information theory. It is a deterministic algorithm leading to a particular result. But what is reading that program? What is the “computer” that runs it? The cell?

And where is the person using the computer, the one who decides to run the program and decides if the program is useful or not? Where is natural selection?

Look at all the terminology of molecular biology: transcription, translation…those are all terms from information theory, which is linear, deterministic and hierarchical – there is a cause that controls the effect.

Even the “News and Views” article accompanying last week’s two papers (Bass and Takahashi 2011) re-frames the results of the papers into information theory metaphor. All the stuff that is happening in the cytoplasm is referred to as “post-translational” as if it was just something more that DNA “caused,” perhaps a little further downstream than usual.

But it is not. The cycles in the cytoplasm are not caused by anything any piece of DNA did. When in sync, the genetic feedback loops and cytoplasmic clocks work synergistically. But when placed in opposition, the cytoplasmic clock dominates (e.g., determines the phase, period, etc.).

The centrality of the gene in much of biological thinking led to another error that these two papers in Nature just fixed. Because different kingdoms of life (bacteria, protista, plants, fungi and animals) have different clock genes, it was assumed, despite the identical mechanistic logic of the mechanism, that the clock evolved independently several times. Identity of players trumped the mechanism of interaction between them.

But if, as the papers show, all organisms have cytoplasmic clocks based on anti-oxidant enzymes, then this cytoplasmic clock is the scaffolding, the base which allows evolution and replacement of all sorts of clock genes in different groups. As clock genes come and go, they can always latch onto the ever-present cytoplasmic clock. And the organism can keep on ticking regardless of the evolving stage in which any particular clock gene may be. This argues for a single origin of the circadian clock, due to universally adaptive nature of the clock, as postulated by Colin Pittendrigh decades ago.

The clock metaphor

The theory of biological rhythms has benefited immensely from the use of the clock as metaphor. Thinking of biological rhythms in terms of oscillatory theory (borrowed from physics) has allowed us to understand how the biological clock works, how it gets synchronized with the environment (entrainment), and how systems with multiple clocks can act together to produce higher-order phenomena (e.g., photoperiodism – measurement of seasonal changes in daylength).

The clock metaphor was also a key for understanding the mechanism as a collection of interacting cogs and wheels. This was crucial for the discovery of clock genes later on.

But once the number of clock genes was determined to be very small, and the interlocking feedback loops between them became the dominant paradigm for the mechanism, the meaning of the clock metaphor shifted – instead of looking at all the potential cogs and wheels, only those made of or from DNA counted. There is nothing wrong with counting everything – genes, and cytoplasmic elements, and the cell membrane, and the interactions between clock cells in a tissue – as cogs and wheels of the biological clock, but somehow, somewhere, we forgot that and settled for a DNA-only view.

Every metaphor that scientists invent has a heuristic value. The information theoretical thinking about genes sped up the research in genetics and molecular biology. The clock metaphor sped up the circadian research.

But it is always a good idea to sometimes step back and consider if the dominant metaphor is constraining in some ways, if it limits the imagination. I have argued before that an occasional switch to a different circadian metaphor – perhaps player-piano, or endless tape recorder, or Rube-Goldberg Machine, or camshaft, or Moebius strip – can be a good way to look at the problem from a new angle. This can be a very productive endeavor, opening one’s eyes to new angles, starting new avenues of research. Every field of science has its metaphors, and it is always a good idea to sometimes analyze them, and sometimes replace them once they outlive their usefulness.

What metaphors are used by lay audience and the media?

There is a difference between metaphors used by scientists to guide their research programs, and metaphors used by journalists to explain research to lay audiences.

The clock metaphor, for example, means ‘interlocking cogs and wheels to study’ for researchers, but ‘timepiece in your brain that tells you when to wake up and when to fall asleep’ for the audience.

Likewise, the gene-control metaphor is something that is easy to understand for the audience that may be used to a hierachical worldview of top-down control (in society, family, religion, politics, or simplistic mechanics of everyday life). A systems-worldview requires a little bit more tolerance for ambiguity (which not everyone has) and a little more sophisticated understanding as to how complex systems work (i.e., how complex behaviors emerge out of interactions between multiple elements, in which the nature of interactions is more important than the identity and behavior of individual elements).

This is probably why the media reports could not capture the complexity of the findings. It provided an or option instead of an and option – the lay reader is probably going to think that DNA has nothing to do with the clock, instead of understanding that both DNA and other elements of the cell are partners. Still, in the media saturated with “gene for X” stories, an occasional “not in our genes” story is a positive event.

On the other hand, since the early 2000s (once the hype over Human Genome Project died down a little bit), the geneticists have moved away from the gene-control metaphor to some extent. Yes, they still sometimes slip up to old habits of mind (and their terminology shows it) – like when they use the term “post-translational” for everything that does not involve DNA in the cell – but the results of their own studies, from quantitative genetics to bumping into walls in some areas of research, have moved them to a more systems-like thinking. They are reinventing Physiology and calling it Systems Biology. And we are all better off for it. It is a more complete Physiology, with the ‘black box’ now wide open.

Another way that gene-primacy seeps into coverage of science is when new studies using molecular techniques are said to have confirmed the old studies using more traditional methods. For a recent example, see how the hypothesis of butterfly migration and speciation by Nabokov was said to have been confirmed by a recent molecular study. But molecular techniques are new, still being tested, calibrated and evaluated. The Nabokov story is really about well done work from the past using tried and tested old reliable techniques, that was strengthened by the new study and in turn validated the molecular method. Comparative anatomy is what validated the genetic method, not the other way round.

Likewise, in this example in clocks, it is very nice that new techniques repeated the old results. Each strengthens the other. The new study does not confirm the old as much as they all confirm each other. But for those enamored with molecules (or those who always think that new is better than old), this duo of papers will seal the deal if the old papers did not.


To summarize, the publication of these two studies in Nature last week is, in my opinion, quite a milestone in the field. First, it showed how it was possible for the clock to originate only once on Earth yet evolve a number of different molecular elements – the cytoplasmic clock was there all along, keeping time while the genes swapped.

Second, it re-framed the discussion of the mechanism. It forcefully demonstrated what many prior studies did in small increments, but this time with modern techniques we love and with enormous power. By reminding the people in the field that DNA is an important but not sufficient element of the clock, it will hopefully guide future research in a new direction, with a more complete view of the clock, and perhaps may even allow some people to venture out and try other productive metaphors instead.


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O’Neill JS., Gerben van Ooijen, Laura E. Dixon, Carl Troein, Florence Corellou, François-Yves Bouget, Akhilesh B. Reddy and Andrew J. Millar, (2011). Circadian rhythms persist without transcription in a eukaryote, Nature, 469 (554–558), doi:10.1038/nature09654

Page, Terry (2000) A Novel Mechanism for the Control of Circadian Clock Period by Light, J Biol Rhythms April 2000 vol. 15 no. 2 155-162, doi: 10.1177/074873040001500209

Peleg, L., A. Dotan, P. Luzato and I. E. Ashkenazi, (1990a) Hexose monophosphate shunt activities in human erythrocytes during oxidative damage induced by hydrogen peroxide, In Vitro Cellular & Developmental Biology – Plant, Volume 26, Number 10, 978-982, DOI: 10.1007/BF02624472

Peleg, L., A. Dotan, P. Luzato and I. E. Ashkenazi (1990b) Long ultradian rhythms in red blood cells and ghost suspensions: Possible involvement of cell membrane , In Vitro Cellular & Developmental Biology – Plant, Volume 26, Number 10, 978-982, DOI: 10.1007/BF02624472

Roenneberg,Till and Merrow, Martha, (1998) Molecular Circadian Oscillators: An Alternative Hypothesis, J Biol Rhythms, vol. 13, 2: pp. 167-179.

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Roenneberg,Till and Merrow, Martha, (2005) Circadian clocks — the fall and rise of physiology. NATURE REVIEWS MOLECULAR CELL BIOLOGY, VOLUME 6: 965-971

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Runft, Linda L., and Dina F. Mandoli (1996) Coordination of cellular events that precede reproductive onset in Acetabularia acetabulum: evidence for a ‘loop’ in development. Development 122, 1187-1194

Schroedinger, E. (1944). What is Life? Cambridge University Press, Cambridge, UK.

SCHWEIGER, E., H. G. WALRAFF, and H. G. SCHWEIGER (1964b) Endogenous circadian rhythm in cytoplasm of Acetabularia: Influence of the nucleus. Science 61548-665:9.

SWEENEY, B. M. (1974) A physiological model for circadian rhythms from the Acetabularia rhythm paradoxes. Int. J. Chronobiol. 2: 25-33.

SWEENEY, B. M., and F. T. HAXO (1961) Persistence of a photosynthetic rhythm in enucleated Acetabularia. Science 134: 1361-1363.

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Image credits: Red blood cells, Wikimedia Commons; Ostreococcus tauri, The Joint Genome Institute; Acetabularia crenulata, The College of Exploration; graphs – from O’Neill JS, & Reddy AB (2011) and O’Neill JS. et al. 2011; and Transcription-translation Feedback Loop model, Nature Reviews Neuroscience

Three new posts on the SciAm Guest Blog

A very busy day on the Scientific American Guest Blog, especially for a Friday. There are three new posts there today.

First, A plea for basic biology by Holly Bik should be a warning call to universities and funders.

Then, Anecdotes from the Archive: Finding beauty in all of this snow by Mary Karmelek.

Finally, Seth Mnookin slams David Kirby and anti-vaccinationist lies in The Huffington Post and the ongoing fear that vaccines might cause autism.

New posts on the SciAm Guest Blog

Brand new post on the Scientific American Guest Blog today – Paradoxical Polyuria–when it comes to kidneys, sometimes more is less, by Pascale Lane.

And the other day, I posted Anecdotes from the Archive: All clean on the Western Front by Mary Karmelek.

Stay tuned, more to come soon….

In the meantime, read, enjoy, comment and share….

New post on the SciAm Guest Blog

New post on the Scientific American Guest Blog! Today, my old Scibling Karen Ventii contributes: Personalizing Cancer Medicine. Read, comment, share….

Sigma Xi Pizza Lunch – ‘ Friends or Foes: Social Relationships Among Female Chimpanzees’ with Anne Pusey

To keep keeping you on your toes, we’ll host Pizza Lunch on a Wednesday again this month, rather than on a Tuesday. And it promises to be another good one.

Come hear Anne Pusey, chair of evolutionary anthropology and a James B. Duke professor at Duke, speak at noon Wed., Feb 23 at Sigma Xi. Her talk: Friends or Foes: Social Relationships Among Female Chimpanzees. Pusey has studied competition, cooperation and social bonds in multiple species. Most of her work focuses on our close evolutionary cousins, the chimpanzees. Early in her career, Pusey observed juvenile and adolescent development under the direction of Jane Goodall at Tanzania’s Gombe Stream Reserve. She still has ties. Her research team maintains and digitizes data collected at Gombe, where Goodall started observing chimpanzees more than 50 years ago.

Thanks to a grant from the N.C. Biotechnology Center, American Scientist Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might want to attend. RSVPs are required (for the slice count) to

Directions to Sigma Xi, the Scientific Research Society in RTP, are here:

Open Laboratory 2011 – submissions so far

The submission form for the 2011 edition of Open Lab is now open. Any blog post written since December 1, 2010 is eligible for submission.

We accept essays, stories, poetry, cartoons/comics, original art.

Once you are done submitting your own posts, you can start looking at the others’, including on aggregators like, and

As I always do, I will keep posting the full list of submitted entries once a week until the deadline – see the listing under the fold.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Help us spread the word by displaying these badges (designed by Doctor Zen:

<a href=””&gt<img src=””&gt</a&gt

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Or take the Open Lab 2011 submission bookmarklet – Open Lab – and drag it to your browser’s toolbar to have it always handy as you browse around science blogs.


A Blog Around The Clock (guest-blog at SA Observations): The line between science and journalism is getting blurry….again
A Blog Around The Clock (guest-blog at SA Guest Blog): Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night

American SciCo: Science Online Will Change the World

The Bunsen Boerner: Chemistry: this shit’s important

Context and variation: Iron-deficiency is not something you get just for being a lady
Context and variation: Even when we want something, we need to hide it.

Deep Sea News: DON’T PANIC: Sustainable seafood and the American outlaw
Deep Sea News: How To Cuddle Your Lady Right, by Smoove A

Denim and Tweed: Evolution’s Rainbow, from sparrows’ stripes to lizard lesbianism

Design. Build. Play.: Computers and the Homeless
Design. Build. Play.: Design Fridays: That’s a big prop

Faraday’s Cage is where you put Schroedinger’s Cat: A shocking experience

Georneys: Geology Word of the Week: L is for Lithosphere

Highly Allochthonous: Ten million feet upon the stair
Highly Allochthonous: A flood is a disaster when people are in the way

Lamentations on Chemistry: On the pitfalls of science outreach to the public

Looking For Detachment: Deep Time
Looking For Detachment: Like caterpillars, crawling or marching…

Magma Cum Laude: Eruption rates at volcanoes

NeuroanthropologyHuman (amphibious model): living in and on the water

NeuroDojo: Indie spirit
NeuroDojo: Ptarmigans on ptreadmills

Observations of a Nerd: Reverse Bestiality: When Animals Commit Sexual Assault
Observations of a Nerd (guest-post on Nutrition Wonderland): The Truth About Organic Farming

Occ Psy Dot Com: Within boundaryless contexts, developmental relationships may positively impact upon optimism

Oscillatory Thoughts: How to be a neuroscientist

RRResearch: Arsenic-associated bacteria (NASA’s claims)

Sauropod Vertebra Picture of the Week: Tutorial 12: How to find problems to work on

Scientific American Guest Blog (Rachel Nuwer): When animals attack: Death databases indicate that our fondest phobias may be misdirected
Scientific American Guest Blog (David Manly): Biting the hand that feeds: The evolution of snake venom
Scientific American Guest Blog (David Manly): The Ferret Hunters
Scientific American Guest Blog (Dan Bailey): In search of the origins of warfare in the American Southwest

Sleeping with the Fishes: Self-Help for Seabirds: How to manage your time and outcompete your neighbors for maximum survival

There and (hopefully) back again…: In the shadows of greatness

This is serious monkey business: “Bad-sad-bad” and other responses to death.
This is serious monkey business: Raison d’etre of the female undergraduate primatology blogger.
This is serious monkey business: Is habituation ethically permissible from a biocentric perspective?

This View of Life: Elements of an Effective Public Education Toolkit

Thoughtomics: We Are Nobody: Contingency and Convergence in Evolution

Tooth and Claw: Of Bad Odors and Good Yarns

Uncertain Principles: Science Is Not Irreducibly Complex

Meet me in NYC on Monday at 7

Yes, I will be in NYC next week, #snowmaggedon or not. This will be a very short visit, flying in early Monday morning and leaving Tuesday afternoon, so I will be in town only one night. So let’s make that night a fun night!

Let’s meet at KILLARNEY ROSE this Monday (Feb.7th) at 7pm – upstairs. If you are in NYC and want to meet me and my friends, show up – you don’t need to be a scientist or writer or blogger or tweeterer – everyone is welcome. Let’s have dinner and some liquids and have fun.

New post on the SciAm Guest Blog

We end the week at the Scientific American Guest Blog with another contribution by Mary Karmelek – Anecdotes from the Archive: The Key to Sorting Mail.

Enjoy, comment, share…

Two new posts on the SciAm Guest Blog – psychology of anti-vaccers and movie reviews from Sundance

Two new exciting posts at the Scientific American Guest Blog this morning!

First, in The perception gap: An explanation for why people maintain irrational fears, his second post on the blog, David Ropeik uses research on risk perception to explain anti-vaccinationist behavior – and a commenter repeatedly demonstrates that the thesis of the post is correct ;-)

Then, in her first dispatch from Sundance film festival, old friend Tamara Krinsky reviews two of the movies with a science theme – Science at Sundance, part 1: The Interrupters and Project Nim.

As always: enjoy, comment, share….

Next Raleigh Science Café: Prevention of Heart Disease: Managing Risk Factors

This month’s Science Café (description below) will be held on February 15th at The Irregardless Cafe. We will be meeting Dr. Deepak Pasi from Rex Hospital. Dr Pasi will talk with us about our hearts- how they work and what keeps our vascular systems healthy. I hope that many of you can come – it should be an interesting discussion about a very important topic.

Prevention of Heart Disease: Managing Risk Factors

Tuesday, February 15, 2011

6:30-8:30 p.m. with discussion beginning at 7:00 followed by Q&A

Location: The Irregardless Café, 901 W. Morgan Street, Raleigh, 833-8898

Heart disease is the leading cause of death for both men and women. Why is heart disease different in women versus men? Why are some people more prone to heart disease than others? Is a healthy diet and exercise enough to prevent it? Will statins prevent heart disease in healthy people? What role does second hand smoke really play? Prevention is key to minimizing the impact of heart disease on our bodies, our longevity and our quality of life. We’ll explore the risk factors, the role of genetics and the things we can do to minimize heart disease.

About our Speaker: Deepak Pasi, M.D. is a board certified cardiologist and completed fellowships in both cardiology and interventional cardiology at the University of North Carolina at Chapel Hill. He has practiced cardiology for twenty five years and is a member of Rex Heart & Vascular Specialists in Raleigh.

Please RSVP to

New post on the SciAm Guest Blog

Today on the Scientific American Guest Blog, Mary Karmelek digs into the SA archive for another cool story and photo: Anecdotes from the Archive: A Ride Fit for a Shah. Enjoy, comment, share…