Category Archives: History of Science

The line between science and journalism is getting blurry….again

 

Human #1: “Hello, nice weather today, isn’t it?”

Human #2: “Ummm…actually not. It’s a gray, cold, windy, rainy kind of day!”

Many a joke depends on confusion about the meaning of language, as in the example above. But understanding the sources of such confusion is important in realms other than stand-up comedy, including in the attempts to convey facts about the world to one’s target audience.

In the example above, Human #1 is using Phatic language, sometimes referred to as ‘small talk‘ and usually exemplified, at least in the British Isles, with the talk about the highly unpredictable weather. (image: by striatic on Flickr)

Phatic language

Phatic discourse is just one of several functions of language. Its role is not to impart any factual information, but to establish a relationship between the people. It conveys things like emotional state, relative social status, alliance, intentions and limits to further conversation (i.e., where the speaker “draws the line”).

If a stranger rides into a small town, a carefully chosen yet meaningless phrase establishes a state of mind that goes something like this: “I come in peace, mean no harm, I hope you accept me in the same way”. The response of the local conveys how the town looks at strangers riding in, for example: “You are welcome…for a little while – we’ll feed you and put you up for the night, but then we hope you leave”. (image: Clint Eastwood in ‘Fistful of Dollars’ from Squidoo)

An important component of phatic discourse is non-verbal communication, as the tone, volume and pitch of the voice, facial expression and body posture modify the language itself and confirm the emotional and intentional state of the speaker.

It does not seem that linguistics has an official term for the opposite – the language that conveys only pure facts – but the term usually seen in such discussions (including the domain of politics and campaigning) is “Conceptual language” so this is what I will use here. Conceptual language is what Human #2 in the joke above was assuming and using – just the facts, ma’am.

Rise of the earliest science and journalism

For the sake of this article, I will use two simplified definitions of science and journalism.

Journalism is communication of ‘what’s new’. A journalist is anyone who can say “I’m there, you’re not, let me tell you about it.”

Science is communication of ‘how the world works’. A scientist is anyone who can say “I understand something about the world, you don’t, let me explain it to you”.

Neither definition necessitates that what they say is True, just what they know to the best of their ability and understanding.

Note that I wrote “science is communication”. Yes, science is the process of discovery of facts about the way the world works, but the communication of that discovery is the essential last step of the scientific process, and the discoverer is likely to be the person who understands the discovery the best and is thus likely to be the person with the greatest expertise and authority (and hopefully ability) to do the explaining.

For the greatest part of human history, none of those distinctions made any sense. Most of communication contained information about what is new, some information about the way the world works, and a phatic component. Knowing how the world works, knowing what is happening in that world right now, and knowing if you should trust the messenger, were all important for survival.

For the most part, the information was local, and the messengers were local. A sentry runs back into the village alerting that a neighboring tribe, painted with war-paints, is approaching. Is that person a member of your tribe, or a stranger, or the well-known Boy Who Cried Wolf? What do you know about the meaning of war-paint? What do you know about the neighboring tribe? Does all this information fit with your understanding of the world? Is information coming from this person to be taken seriously? How are village elders responding to the news? Is this piece of news something that can aid in your personal survival?

For the longest time, information was exchanged between people who knew each other to some degree – family, neighbors, friends, business-partners. Like in a fishing village, the news about the state of fishing stocks coming from the ships at sea is important information exchanged at the local tavern. But is that fish-catch information ‘journalism’ (what’s new) or ‘science’ (how the world works)? It’s a little bit of both. And you learn which sailors to trust by observing who is trusted by the locals you have already learned to trust. Trust is transitive.

Someone in the “in-group” is trusted more than a stranger – kids learned from parents, the community elders had the authority: the trust was earned through a combination of who you are, how old you are, and how trustworthy you tended to be in the past. New messengers are harder to pin down on all those criteria, so their information is taken with a degree of skepticism. The art of critical thinking (again, not necessarily meaning that you will always pick the Truth) is an ancient one, as it was essential for day-to-day survival. You trust your parents (or priests or teachers) almost uncritically, but you put up your BS filters when hearing a stranger.

Emergence of science and of journalism

The invention of the printing press precipitated the development of both journalism and science. But that took a very long time – almost two centuries (image: 1851, printing press that produced early issues of Scientific American). After Gutenberg printed the Bible, most of what people printed were political pamphlets, church fliers and what for that time and sensibilities went for porn.

London Gazette of 1666 is thought to be the first newspaper in the modern sense of the word. (image: from DavidCo) Until then, newspapers were mostly irregular printings by individuals, combining news, opinion, fiction and entertainment. After this, newspapers gradually became regular (daily, weekly, monthly) collections of writings by numerous people writing in the same issue.

The first English scientific journal was published a year before – the Philosophical Transactions of the Royal Society of London in 1665 (image: Royal Society of London).

Until then, science was communicated by letters – those letters were often read at the meetings of scientists. Those meetings got formalized into scientific societies and the letters read at such meetings started getting printed. The first scientific journals were collections of such letters, which explains why so many journals have the words “Letters”, “Annals” or “Proceedings” in their titles.

Also, before as well as for a quite a long time after the inception of first journals, much of science was communicated via books – a naturalist would spend many years collecting data and ideas before putting it all in long-form, leather-bound form. Those books were then discussed at meetings of other naturalists who would often respond by writing books of their own. Scientists at the time did not think that Darwin’s twenty-year wait to publish The Origin was notable (William Kimler, personal communication) – that was the normal timeline for research and publishing at the time, unusual only to us from a modern perspective of 5-year NIH grants and the ‘publish or perish’ culture.

As previously oral communication gradually moved to print over the centuries, both journalistic and scientific communication occured in formats – printed with ink on paper – very similar to blogging (that link leads to the post that served as a seed from which this article grew). If born today, many of the old writers, like Montaigne, would be Natural Born Bloggers (‘NBBs’ – term coined by protoblogger Dave Winer). A lot of ship captains’ logs were essentially tweets with geolocation tags.

People who wanted to inform other people printed fliers and pamphlets and books. Personal letters and diaries were meant to be public: they were as widely shared as was possible, they were publicly read, saved, then eventually collected and published in book-form (at least posthumously). Just like blogs, tweets and Facebook updates today….

The 18th century ‘Republic of Letters’ (see the amazing visualization of their correspondence) was a social network of intellectual leaders of Europe who exchanged and publicly read their deep philosophical thoughts, scientific ideas, poetry and prose.

Many people during those centuries wrote their letters in duplicate: one copy to send, one to keep for publishing Collected Letters later in life. Charles Darwin did that, for example (well, if I remember correctly, his wife made copies from his illegible originals into something that recipients could actually read), which is why we have such a complete understanding of his work and thought – it is all well preserved and the availability of such voluminouos correspondence gave rise to a small industry of Darwinian historical scholarship.

What is important to note is that, both in journalism and in science, communication could be done by anyone – there was no official seal of approval, or licence, to practice either of the two arts. At the same time, communication in print was limited to those who were literate and who could afford to have a book printed – people who, for the most part, were just the wealthy elites. Entry into that intellectual elite from a lower social class was possible but very difficult and required a lot of hard work and time (see, for example, a biography of Alfred Russell Wallace). Membership in the worlds of arts, science and letters was automatic for those belonging to the small group of literate aristocracy. They had no need to establish formalized gatekeeping as bloodlines, personal sponsorship and money did the gatekeeping job quite well on their own.

As communication has moved from local to global, due to print, trust had to be gained over time – by one’s age, stature in society, track record, and by recommendation – who the people you trust say you should trust. Trust is transitive.

Another thing to note is that each written dispatch contained both ‘what’s new’ and ‘how the world works’ as well as a degree of phatic discourse: “This is what happened. This is what I think it means. And this is who I am so you know why you should trust me.” It is often hard to tell, from today’s perspective, what was scientific communication and what was journalism.

Personal – and thus potentially phatic – communication was a norm in the early scientific publishing. For example, see “A Letter from Mr J. Breintal to Peter Collinfoxl, F. RXS. contairnng an Account of what he felt after being bit by a Rattle-fnake” in Philosophical Transactions, 1747. – a great account of it can be found at Neurotic Physiology. It is a story of a personal interaction with a rattlesnake and the discovery leading from it. It contained “I was there, you were not, let me tell you what happened” and “I understand something, you don’t, let me explain that to you” and “Let me tell you who I am so you can know you can trust me”.

Apparently, quite a lot of scientific literature of old involved exciting narratives of people getting bitten by snakes – see this one from 1852 as well.

The anomalous 20th century – effects of technology

The gradual changes in society – invention of printing, rise of science, rise of capitalism, industrial revolution, mass migration from rural to urban areas, improvements in transportation and communication technologies, to name just a few – led to a very different world in the 20th century.

Technology often leads societal changes. If you were ever on a horse, you understand why armies that used stirrups defeated the armies that rode horses without this nifty invention.

Earlier, the speed of spreading news was much slower (see image: Maps of rates of travel in the 19th century – click on the link to see bigger and more). By 1860 Telegraph reached to St. Louis. During its short run the Pony Express could go the rest of the way to San Francisco in 10 days. After that, telegraph followed the rails. First transcontinental line was in 1869. Except for semaphores (1794) information before the telegraph (1843) could only travel as fast as a rider or boat (Thanks to John McKay for this brief primer on the history of speed of communication in Northern America. I am assuming that Europe was slightly ahead and the rest of the world somewhat behind).

The 20th century saw invention or improvement of numerous technologies in transportation – cars, fast trains, airplanes, helicopters, space shuttles – and in communication – telephone, radio, and television. Information could now travel almost instantly.

But those new technologies came with a price – literally. While everyone could write letters and send them by stagecoach, very few people could afford to buy, run and serve printing presses, radio stations and television studios. These things needed capital, and increasingly became owned by rich people and corporations.

Each inch of print or minute of broadcast costs serious money. Thus, people were employed to become official filters of information, the gatekeepers – the editors who decided who will get access to that expensive real estate. As the editors liked some people’s work better than others, those people got employed to work in the nascent newsrooms. Journalism became professionalized. Later, universities started journalism programs and codified instruction for new journalists, professionalizing it even more.

Instead of people informing each other, now the few professionals informed everyone else. And the technology did not allow for everyone else to talk back in the same medium.

The broadcast media, a few large corporations employing professional writers informing millions – with no ability for the receivers of information to fact-check, talk back, ask questions, be a part of the conversation – is an exception in history, something that lasted for just a few decades of the 20th century.

The anomalous 20th century – industrialization

Industrial Revolution brought about massive migration of people into big cities. The new type of work required a new type of workforce, one that was literate and more educated. This led to the invention of public schools and foundation of public universities.

In the area of science, many more people became educated enough (and science still not complex and expensive yet) to start their own surveys, experiments and tinkering. The explosion of research led to an explosion of new journals. Those too became expensive to produce and started requiring professional filters – editors. Thus scientific publishing also became professionalized. Not every personal anecdote could make it past the editors any more. Not everyone could call oneself a scientist either – a formal path emerged, ending with a PhD at a university, that ensured that science was done and published by qualified persons only.

By the 1960s, we got a mass adoption of peer-review by scientific journals that was experimentally done by some journals a little earlier. Yes, it is that recent! See for example this letter to Physical Review in 1936:

 

Dear Sir,

We (Mr. Rosen and I) had sent you our manuscript for publication and had not authorized you to show it to specialists before it is printed. I see no reason to address the — in any case erroneous — comments of your anonymous expert. On the basis of this incident I prefer to publish the paper elsewhere.

Respectfully,

Albert Einstein

Or this one:

 

John Maddox, former editor of Nature: The Watson and Crick paper was not peer-reviewed by Nature… the paper could not have been refereed: its correctness is self-evident. No referee working in the field … could have kept his mouth shut once he saw the structure…

Migration from small towns into big cities also meant that most people one would meet during the day were strangers. Meeting a stranger was not something extraordinary any more, so emergence and enforcement of proper proscribed conduct in cities replaced the need for one-to-one encounters and sizing up strangers using phatic language. Which is why even today phatic language is much more important and prevalent in rural areas where it aids personal survival than in urban centers where more general rules of behavior among strangers emerged (which may partially explain why phatic language is generally associated with conservative ideology and conceptual language with politicial liberalism, aka, the “reality-based community“).

People moving from small hometowns into big cities also led to breaking up of families and communities of trust. One needed to come up with new methods for figuring out who to trust. One obvious place to go was local media. They were stand-ins for village elders, parents, teachers and priests.

If there were many newspapers in town, one would try them all for a while and settle on one that best fit one’s prior worldview. Or one would just continue reading the paper one’s parents read.

But other people read other newspapers and brought their own worldviews into the conversation. This continuous presence of a plurality of views kept everyone’s BS filters in high gear – it was necessary to constantly question and filter all the incoming information in order to choose what to believe and what to dismiss.

The unease with the exposure to so many strangers with strange ideas also changed our notions of privacy. Suddenly we craved it. Our letters are now meant for one recepient only, with the understanding it will not be shared. Personal diaries now have lockets. After a century of such craving for privacy, we are again returning to a more historically traditional notions, by much more freely sharing our lives with strangers online.

The anomalous 20th century – cleansing of conceptual language in science and journalism

Until the 20th century we did not see the consolidation of media into large conglomerates, and of course, there were no mass radio or TV until mid-20th century. Not until later in the century did we see the monopolization of local media markets by a single newspaper (competitors going belly-up) which, then, had to serve everyone, so it had to invent the fake “objective” HeSaidSheSaid timid style of reporting in order not to lose customers of various ideological stripes and thus lose advertising revenue.

Professionalising of journalism, coupled with the growth of media giants serving very broad audiences, led to institutionalization of a type of writing that was very much limited to “what’s new”.

The “let me explain” component of journalism fell out of favor as there was always a faction of the audience that had a problem with the empirical facts – a faction that the company’s finances could not afford to lose. The personal – including phatic – was carefully eliminated as it was perceived as unobjective and inviting the criticism of bias. The way for a reporter to inject one’s opinion into the article was to find a person who thinks the same in order to get the target quote. A defensive (perhaps cowardly) move that became the norm. And, once the audience caught on, led to the loss of trust in traditional media.

Reduction of local media to a single newspaper, a couple of local radio stations and a handful of broadcast TV channels (that said esentially the same thing), left little choice for the audience. With only one source in town, there was no opportunity to filter among a variety of news sources. Thus, many people started unquestioningly accepting what 20th-century style broadcast media served them.

Just because articles were under the banners of big companies did not make them any more trustworthy by definition, but with no alternative it is still better to be poorly informed than not informed at all. Thus, in the 20th century we gradually lost the ability to read everything critically, awed by the big names like NYT and BBC and CBS and CNN. Those became the new parents, teachers, tribal elders and priests, the authority figures whose words are taken unquestioningly.

In science, explosion in funding not matched by explosion of job positions, led to overproduction of PhDs and a rise of hyper-competitive culture in academia. Writing books became unproductive. The only way to succeed is to keep getting grants and the only way to do that is to publish very frequently. Everything else had to fall by the wayside.

False measures of journal quality – like the infamous Impact Factor – were used to determine who gets a job and tenure and who falls out of the pipeline. The progress of science led inevitably to specialization and to the development of specialized jargon. Proliferation of expensive journals ensured that nobody but people in highest-level research institutions had access to the literature, so scientists started writing only for each other.

Scientific papers became dense, but also narrowed themselves to only “this is how the world works”. The “this is new” became left out as the audience already knew this, and it became obvious that a paper would not be published if it did not produce something new, almost by definition.

And the personal was so carefully excised for the purpose of seeming unbiased by human beings that it sometimes seems like the laboratory equipment did all the experiments of its own volition.

So, at the close of the 20th century, we had a situation in which journalism and science, for the first time in history, completely separated from each other. Journalism covered what’s new without providing the explanation and context for new readers just joining the topic. Science covered only explanation and only to one’s peers.

In order to bridge that gap, a whole new profession needed to arise. As scientists understood the last step of the scientific method – communication – to mean only ‘communication to colleagues’, and as regular press was too scared to put truth-values on any statements of fact, the solution was the invention of the science journalist – someone who can read what scientists write and explain that to the lay audience. With mixed success. Science is hard. It takes years to learn enough to be able to report it well. Only a few science journalists gathered that much expertise over the years of writing (and making mistakes on the way).

So, many science journalists fell back on reporting science as news, leaving the explanation out. Their editors helped in that by severely restricting the space – and good science coverage requires ample space.

A good science story should explain what is known by now (science), what the new study brings that is new (news) and why does that matter to you (phatic discourse). The lack of space usually led to omission of context (science), shortening of what is new (news) and thus leaving only the emotional story intact. Thus, the audience did not learn much, Certainly not enough to be able to evaluate next day’s and next week’s news.

This format also led to the choice of stories. It is easy to report in this way if the news is relevant to the audience anyway, e.g., concerning health (the “relevant” stories). It is also easy to report on misconduct of scientists (the “fishy” stories) – which is not strictly science reporting. But it was hard to report on science that is interesting for its own sake (the “cool” stories).

What did the audience get out of this? Scientists are always up to some mischief. And every week they change the story as to what is good or bad for my health. And it is not very fun, entertaining and exciting. No surprise that science as endeavour slowly started losing trust with the (American) population, and that it was easy for groups with financial, political or religious interests to push anti-science rhetoric on topics from hazards of smoking to stem-cell research to evolution to climate change.

At the end of the 20th century, thus, we had a situation in which journalism and science were completely separate endeavors, and the bridge between them – science journalism – was unfortunately operating under the rules of journalism and not science, messing up the popular trust in both.

Back to the Future

It is 2010. The Internet has been around for 30 years, the World Wide Web for 20. It took some time for the tools to develop and spread, but we are obviously undergoing a revolution in communication. I use the word “revolution” because it is so almost by definition – when the means of production change hands, this is a revolution.

The means of production, in this case the technology for easy, cheap and fast dissemination of information, are now potentially in the hands of everyone. When the people formerly known as the audience employ the press tools they have in their possession to inform one another, we call that ‘citizen journalism.’ And some of those citizens possess much greater expertise on the topics they cover than the journalists that cover that same beat. This applies to science as well.

In other words, after the deviation that was the 20th century, we are going back to the way we have evolved as a species to communicate – one-to-one and few-to-few instead of one-to-many. Apart from technology (software instead of talking/handwriting/printing), speed (microseconds instead of days and weeks by stagecoach, railroad or Pony Express, see image above) and the number of people reached (potentially – but rarely – millions simultaneously instead of one person or small group at a time), blogging, social networking and other forms of online writing are nothing new – this is how people have always communicated. Like Montaigne. And the Republic of Letters in the 18th century. And Charles Darwin in the 19th century.

All we are doing now is returning to a more natural, straightforward and honest way of sharing information, just using much more efficient ways of doing it. (Images from Cody Brown)

And not even that – where technology is scarce, the analog blogging is live and well (image: Analog blogger, from AfriGadget).

What about trustworthiness of all that online stuff? Some is and some isn’t to be trusted. It’s up to you to figure out your own filters and criteria, and to look for additional sources, just like our grandparents did when they had a choice of dozens of newspapers published in each of their little towns.

With the gradual return of a more natural system of communication, we got to see additional opinions, the regular fact-checks on the media by experts on the topic, and realized that the mainstream media is not to be trusted.

With the return of a more natural system of communication, we will all have to re-learn how to read critically, find second opinions, evaluate sources. Nothing new is there either – that is what people have been doing for millennia – the 20th century is the exception. We will figure out who to trust by trusting the judgment of people we already trust. Trust is transitive.

Return of the phatic language

What does this all mean for the future of journalism, including science journalism?

The growing number of Web-savvy citizens have developed new methods of establishing trustworthiness of the sources. It is actually the old one, pre-20th century method – relying on individuals, not institutions. Instead of treating WaPo, Fox, MSNBC and NPR as the proxies for the father, teacher, preacher and the medicine man, we now once again evaulate individuals.

As nobody enters a news site via the front page and looks around, but we all get to individual articles via links and searches, we are relying on bylines under the titles, not on the logos up on top. Just like we were not born trusting NYTimes but learned to trust it because our parents and neighbors did (and then perhaps we read it for some time), we are also not born knowing which individuals to trust. We use the same method – we start with recommendations from people we already trust, then make our own decisions over time.

If you don’t link to your sources, including to scientific papers, you lose trust. If you quote out of context without providing that context, you lose trust. If you hide who you are and where you are coming from – that is cagey and breeds mistrust. Transparency is the new objectivity.

And transparency is necessarily personal, thus often phatic. It shows who you are as a person, your background, your intentions, your mood, your alliances, your social status.

There are many reasons sciencebloggers are more trusted than journalists covering science.

First, they have the scientific expertise that journalists lack – they really know what they are talking about on the topic of their expertise and the audience understands this.

Second, they link out to more, more diverse and more reliable sources.

Third, being digital natives, they are not familiar with the concept of word-limits. They start writing, they explain it as it needs to be explained and when they are done explaining they end the post. Whatever length it takes to give the subject what it’s due.

Finally, not being trained by j-schools, they never learned not to let their personality shine through their writing. So they gain trust by connecting to their readers – the phatic component of communication.

Much of our communication, both offline and online, is phatic. But that is necessary for building trust. Once the trust is there, the conceptual communication can work. If I follow people I trust on Twitter, I will trust that they trust the sources they link to so I am likely to click on them. Which is why more and more scientists use Twitter to exchage information (PDF). Trust is transitive.

Scientists, becoming journalists

Good science journalists are rare. Cuts in newsrooms, allocation of too little space for science stories, assigning science stories to non-science journalists – all of these factors have resulted in a loss of quantity and quality of science reporting in the mainstream media.

But being a good science journalist is not impossible. People who take the task seriously can become experts on the topic they cover (and get to a position where they can refuse to cover astronomy if their expertise is evolution) over time. They can become temporary experts if they are given sufficient time to study instead of a task of writing ten stories per day.

With the overproduction of PhDs, many scientists are choosing alternative careers, including many of them becoming science writers and journalists, or Press Information Officers. They thus come into the profession with the expertise already there.

There is not much difference between a research scientist who blogs and thus is an expert on the topic s/he blogs about, and a research scientist who leaves the lab in order to write as a full-time job. They both have scientific expertise and they both love to write or they wouldn’t be doing it.

Blog is software. A medium. One of many. No medium has a higher coefficient of trustworthiness than any other. Despite never going to j-school and writing everything on blogs, I consider myself to be a science writer.

Many science journalists, usually younger though some of the old ones caught on quickly and became good at it (generation is mindset, not age), grok the new media ecosystem in which online collaboration between scientists and journalists is becoming a norm.

At the same time, many active scientists are now using the new tools (the means of production) to do their own communication. As is usually the case with novelty, different people get to it at different rates. The conflicts between 20th and 21st style thinking inevitably occur. The traditional scientists wish to communicate the old way – in journals, letters to the editor, at conferences. This is the way of gatekeeping they are used to.

But there have been a number of prominent cases of such clashes between old and new models of communication, including the infamous Roosevelts on toilets (the study had nothing to do with either US Presidents or toilets, but it is an instructive case – image by Dr.Isis), and several other smaller cases.

The latest one is the Arsenic Bacteria Saga in which the old-timers do not seem to undestand what a ‘blog’ means, and are seemingly completely unaware of the important distinction between ‘blogs’ and ‘scienceblogs’, the former being online spaces by just about anyone, the latter being blogs written by people who actually know their science and are vetted or peer-reviewed in some way e.g., at ResearchBlogging.org or Scienceblogging.org or by virtue of being hand-picked and invited to join one of the science blogging networks (which are often run by traditional media outlets or scientific publishers or societies) or simply by gaining resepect of peers over time.

Case by case, old-time scientists are learning. Note how both in the case of Roosevelts on toilets and the Arsenic bacteria the initially stunned scientists quickly learned and appreciated the new way of communication.

In other words, scientists are slowly starting to get out of the cocoon. Instead of just communicating to their peers behind the closed doors, now they are trying to reach out to the lay audience as well.

As more and more papers are Open Access and can be read by all, they are becoming more readable (as I predicted some years ago). The traditional format of the paper is changing. So they are covering “let me explain” portion better, both in papers and on their own blogs.

They may still be a little clumsy about the “what’s new” part, over-relying on the traditional media to do it for them via press releases and press conferences (see Darwinius and arsenic bacteria for good examples) instead of doing it themselves or taking control of the message (though they do need to rely on MSM to some extent due to the distinction between push and pull strategies as the media brands are still serving for many people as proxies for trustworthy sources).

But most importantly, they are now again adding the phatic aspect to their communication, revealing a lot of their personality on social networks, on blogs, and even some of them venturing into doing it in scientific papers.

By combining all three aspects of good communication, scientists will once again regain the trust of their audience. And what they are starting to do looks more and more like (pre-20th century) journalism.

Journalists, becoming scientists

On the other side of the divide, there is a renewed interest in journalism expanding from just “this is new” to “let me explain how the world works”. There are now efforts to build a future of context, and to design explainers.

If you are not well informed on an issue (perhaps because you are too young to remember when it first began, or the issue just started being relevant to you), following a stream of ‘what is new’ articles will not enlighten you. There is not sufficient information there. There is a lot of tacit knowledge that the writer assumes the readers possess – but many don’t.

There has to be a way for news items to link to some kind of collection of background information – an ‘explainer’. Such an explainer would be a collection of verifiable facts about the topic. A collection of verifiable facts about the way the world works is….scientific information!

With more and more journalists realizing they need to be transparent about where they are coming from, injecting personality into their work in order to build trust, some of that phatic language is starting to seep in, completing the trio of elements of effective communication.

Data Journalism – isn’t this science?

Some of the best journalism of the past – yes, the abominable 20th century – was done when a reporter was given several months to work on a single story requiring sifting through boxes and boxes of documents. The reporter becomes the expert on the topic, starts noticing patterns and writes a story that brings truly new knowledge to the world. That is practically science! Perhaps it is not the hardest of the hard sciences like physics, but as good as well-done social science like cultural anthropology, sociology or ethnography. There is a system and a method very much like the scientific method.

Unfortunately, most reporters are not given such luxury. They have to take shortcuts – interviewing a few sources to quote for the story. The sources are, of course, a very small and very unrepresentative sample of the relevant population – from a rolodex. Call a couple of climate scientists, and a couple of denialists, grab a quote from each and stick them into a formulaic article. That is Bad Science as well as Bad Journalism. And now that the people formerly known as audience, including people with expertise on the topic, have the tools to communicate to the world, they often swiftly point out how poorly such articles represent reality.

But today, most of the information, data and documents are digital, not in boxes. They are likely to be online and can be accessed without travel and without getting special permissions (though one may have to steal them – as Wikileaks operates: a perfect example of the new data journalism). Those reams of data can be analyzed by computers to find patterns, as well as by small armies of journalists (and other experts) for patterns and pieces of information that computer programs miss.

This is what bioinformaticists do (and have already built tools to do it – contact them, steal their tools!).

Data journalism. This is what a number of forward-thinking journalists and media organizations are starting to do.

This is science.

On the other hand, a lot of distributed, crowdsourced scientific research, usually called Citizen Science, is in the business of collecting massive amounts of data for analysis. How does that differ from data journalism? Not much?

Look at this scientific paper – Coding Early Naturalists’ Accounts into Long-Term Fish Community Changes in the Adriatic Sea (1800–2000) – is this science or data journalism? It is both.

The two domains of communicating about what is new and how the world works – journalism and science – have fused again. Both are now starting to get done by teams that involve both professionals and amateurs. Both are now led by personalities who are getting well-known in the public due to their phatic communication in a variety of old and new media.

It is important to be aware of the shortness of our lives and thus natural tendency for historical myopia. Just because we were born in the 20th century does not mean that the way things were done then are the way things were ‘always done’, or the best ways to do things – the pinnacle of cultural and social development. The 20th century was just a strange and deviant blip in the course of history.

As we are leaving the 20th century behind with all of its unusual historical quirks, we are going back to an older model of communicating facts – but with the new tools we can do it much better than ever, including a much broader swath of society – a more democratic system than ever.

By the way, while it’s still cold, the rain has stopped. And that is Metaphorical language…

This article was commissioned by Science Progress and will also appear on their site in 24 hours.

A Missing Link Found (and subsequently Lost) at the SciAm Guest Blog

Here is a treat for you at the Scientific American Guest Blog. Today’s contribution is by Brian Switek – check out Breaking Our Link to the March of Progress. Read, enjoy, comment (at the registration the system suggests that you need a confirmation e-mail – you don’t, just log in and start posting).

Written In Stone: interview with Brian Switek

2010 is an incredible year for science books, many written by people who daily write on blogs.

The latest in this fantastic streak is Written In Stone (homepage, IndieBound, Amazon) by Brian Switek (blog, Twitter).

Written In Stone is officially published today. If you pre-ordered it, it should hit your mailbox in a few days and bookstores should get it soon after (watch Brian’s blogs for updates – there was a small delay in shipping). I got the book earlier, have read it and loved it – my review is coming here later today. But first, I wanted to catch up with Brian and ask him a few questions about his book, his blog, and how the two are connected.

———–

A few years ago, you were a student and blogging was a hobby – something you did on the side, out of love. At what point did you realize that you could do writing as a profession? Was there a precipitating event or did that gradually dawn on you?

There wasn’t any single event or cause – I just fell into it. Now that we’re mostly beyond the blogger vs. journalist sniping – I hope – I can look back and say that I was acting like a science writer even before it became a viable career option. Making the transition required a change in attitude and a realization that I could actually get paid for what I like to do, and I feel exceptionally lucky that I have been able to turn my hobby into a nascent science writing career (even though I still work an unrelated day job to keep the lights on at home).

The more detailed story goes like this – After blogging for two years, I got serious about my science writing and started to pitch to magazines. My performance was abysmal. Most of the time I didn’t even hear back from the publications I pitched to. Still, I kept using my blog as a writing laboratory and tried to fine-tune my writing. Then, in May of last year, everything changed almost instantaneously. It was at that time that I started working with my literary agent – Peter Tallack of the Science Factory – and Mark Henderson of the Times was kind enough to give me my first formal op-ed about the Darwinius controversy. Those breakthroughs, paired with the earlier acceptance of my first academic paper (just published), allowed me to build up enough momentum to start making some headway into more formal channels of science writing outside the blogohedron.

I wouldn’t be able to do what I do without blogs, Twitter, or the web in general. Blogging allowed me to practice writing, plug into a community of fellow science enthusiasts, and has otherwise made it possible for me to become a professional – if still part-time – science writer. If I tried to do the same thing just a few years ago, or otherwise tried to jump into science writing without developing my writing online, I would have almost surely failed. As I mentioned above, though, I did not think of my efforts as a career change. The only major difference was that people started paying me for the sort of work I had been doing anyway!

How did you decide to write a book? You were already a well-known blogger and have started appearing in more mainstream media on occasion – why a book?

Written in Stone had a relatively long gestation and significantly changed since the time that I was first inspired to write a book. I knew that I wanted to write a book about evolution from the time I started blogging, but I was pretty clueless as to how to go about it. I used my blog as a way to practice writing, keep up with the literature, and organize my ideas. Blogging gave me an incentive to keep learning, researching, and sharing that information with whoever cared to read it.

This went on for about three years. I kept notes and wrote parts of a few chapters, but I didn’t have a story to tie things all together. I knew that I wanted to write about evolution from the perspective of the fossil record, but that’s not a book – I needed a more specific angle from which to approach the bigger story of life through time. I knew that I didn’t want to write a comprehensive textbook – we’ve already got plenty of those – but what examples should I choose to help people understand what fossils tell us about how life has changed?

Unfortunately I can’t remember the moment the idea struck me, but I settled on looking at some of the major transitions in the history of vertebrates that transfixed me as a child. The evolution of the first tetrapods from fish, the evolution of birds from dinosaurs, the evolution of whales from terrestrial mammals, the evolution of humans, and others – they were classic examples of evolutionary change, but as I became more familiar with the scientific literature I felt that the public wasn’t being presented with the latest science about these examples. Even in recent popular books about evolution, a few of these transitions would be presented but usually in such paltry detail as to be unconvincing to anyone who didn’t already agree that evolution is a reality. More than that, these changes have been debated for a very long time but we often talk about them only in reference to recent discoveries. I wanted to dig into the long history of debate and show how our understanding has changed. In distilling everything down to simple, step-by-step diagrams of evolutionary change, I felt like other authors had missed something, and I wanted to plug that gap in the popular literature.

Once I figured all that out, writing the book wasn’t too difficult. I had been rummaging through the literature for my own education for several years already – it was mostly a matter of writing the thing. With three chapters in hand, I signed with Bellevue Literary Press in September and completed the first full draft of the manuscript just two days before Christmas. The manuscript went back and forth a few times over the following months for edits, but, looking back, I am still a little baffled as to how I put the whole thing together so quickly!

Your writing – both on the blog and in the book – looks at evolution, focusing mainly on fossils, in the context of history of science. This is a pretty unique combination of themes – where did that come from? Was that a conscious decision or something that just happened as it combined your existing passions?

The mix of evolution, paleontology, and the history of science happened organically. They all overlap and feed into each other. Since I wanted to write about what the fossil record tells us about evolution, those aspects of the story came together very easily. I could have left it at that, but then I would have done the same thing as everyone else by divorcing recent discoveries from their context. I didn’t want to do that. I did not want to act as a figure of authority, handing down data for the public to digest and accept.

Instead of taking the more traditional approach, I wanted to give the book a warmer tone – I wanted to present science in the way that I might talk to a curious friend about evolution, or in terms of what I might say if I were walking with someone through a natural history museum. The history of science allowed me to do this by providing me with a flowing narrative which encompassed the scientific points I wanted to talk about. This served the dual purpose of placing recent discoveries in context and also gave me a way to lead readers through the tangled process of scientific discovery. This was especially important in the historical chapters about the beginnings of paleontology and evolutionary theory (Ch. 2 and 3). I found the idea of simply laying out the nuts and bolts of stratigraphy, natural selection, the nature of the fossil record, etc. repulsive – as I mentioned, I had no intention of writing a textbook – but by tracing the history of science I could use stories to introduce readers to those same concepts in a more palatable way.

Naturally, my own interests played a role, as well. I am fascinated by vertebrate paleontology, and both evolutionary theory and the history of science remain important in the field for understanding the patterns of life on earth and how our perspective of those patterns has changed. It was not a stretch to bring it all together. Paleontology is an evolutionary science, and paleontologists are constantly reexamining old specimens and localities. Given all these available perspectives, it was mostly a matter of choosing where to place the emphasis.

The book grew out of your blog. What proportion of the book, can you estimate, comes directly from edits of your older posts, and how much was brand new material? Was it difficult to repurpose the bloggy format into something that will work well in the book form?

The book grew out of my blog in the sense that I used my blog to practice writing about some studies and ideas which eventually became incorporated into the blog. The book is not just a stitched-together collection of posts. It was written as a story unto itself – containing many smaller stories – and even when I covered something I had blogged about earlier I disregarded what I had already said and wrote something fresh. Sometimes I would dig back into my posts for something I had referenced which I had trouble remembering, but in no instance did I edit any of my posts to place that material in the book. I wanted to write in such a way that the story flowed, and I felt that if I was going to start incorporating material directly plucked from the blog I would jeopardize that. Readers of my blogs will see some familiar subjects, absolutely, but, barring quotations, the book is 100% new writing.

Reading the book, it struck me how unique it is and how much it fills a glaring gap in the literature. There are many books on evolution. There are many books on the history of science. There are many books about fossils (though usually narrower in subject, focusing on a single group like dinosaurs, or even a single fossil like Tiktaalik or Darwinius). Yet I cannot remember another book that combines these three topics until today (literally today!). While it is fortunate for you that this niche was wide open for you to fill, do you have any thoughts as to why this niche was empty to begin with? Aren’t there other scholars who could have, perhaps should have, covered this area in this way?

I think some historians of science have written similar books, but they have usually been focused on a particular time period of group of researchers (such as Adrian Desmond’s Archetypes and Ancestors about Victorian paleontology, Peter Bowler’s Life’s Splendid Drama about early 20th-century paleontology, or Eric Buffetaut’s sadly out-of-print A Short History of Vertebrate Paleontology). When you’re dealing with the history of paleontology, you have to include biological details as well as historical ones, and in many ways this historical subgenre was very influential in determining how I should go about telling my story.

You’re absolutely right about the gap in the literature, though. I intentionally wrote this book to fill it. There’s no single reason why the gap was left open to start with. From a practical perspective, the history of science is often left out of popular books because there is a common assumption that the public doesn’t care about it. One publisher I spoke to about the book early on, in fact, wanted me to cut all the historical material from the book and focus only on new discoveries – from science magazines to book publishers, there is a major push to cover what is new and exciting and leave the historical bits for people who want to track them down (despite the success of some books, such as Bill Bryson’s A Short History of Nearly Everything, which have a heavy emphasis on history!). An exception is Sean B. Carroll’s recent book Remarkable Creatures, but, while I greatly enjoyed it, the treatment of significant people and specimens was a collection of snapshots which did not illustrate the importance of paleontology to our understanding of evolution. There are gaps and jumps in my narrative too – if I included everything I wanted Written in Stone would have rivaled The Structure of Evolutionary Theory in length – but it was very important to me to trace ideas through multiple shifts in understanding over the past 150 years.

The fact that many recent, popular-audience books about evolution – such as Why Evolution is True by Jerry Coyne, The Greatest Show on Earth by Richard Dawkins, and Only a Theory by Kenneth Miller – have been written by lab-based evolutionary scientists is another reason for the persistence of the “paleo gap.” Paleontology isn’t their field and so, understandably, doesn’t get much attention from these authors outside of transitional forms in the fossil record. More than that, though, there is something of a conceit that genetics and microbiology are more important to evolutionary science than paleontology is. Paleontology is still often viewed as the search for old bones to fill museums with – it can demonstrate the reality of evolution by do little else. This appraisal of paleontology has been around since the beginning of the 20th century, at least, and Dawkins even downplayed the importance of the fossil record to understanding evolution in his book The Ancestor’s Tale.

Since Stephen Jay Gould died in 2002, we haven’t really had a strong public advocate for paleontology as an essential evolutionary science. I’m no Gould, but I was inspired by his work to communicate the relevance of the fossil record to understanding of evolution (as well as similar efforts made before him by George Gaylord Simpson). Not only does paleontology provide the essential context to understand why life is as it is now – it is the science which showed us that extinction is real and that life has been changing for vast periods of time – but has become arguably the most interdisciplinary evolutionary science. Paleontologists regularly use ideas and techniques from genetics, molecular biology, embryology, histology, geochemistry, and other sciences in addition to comparative anatomy and geology. Having just attended the 70th annual meeting of the Society of Vertebrate Paleontology just last month, I can tell you that paleontology is an exceptionally vibrant field in which everything from the color of dinosaur feathers to the tempo and mode of evolutionary change are being investigated. This makes the rather brief treatment of paleontology in many recent books on evolution all the more irritating – paleontology, as I know it, is not being reflected in discussions about evolution, and I wanted to write a book to help remedy that.

One thing that struck me as I was reading the book is how well fleshed are the characters in the story, people like Lamarck, Darwin, Owen and Huxley, among others. You present them with a nuance that is rarely seen in usual discourse on the history of evolution. How much did you use biographies of these people, their letters and diaries, in trying to understand them as complex personalities, not just cardboard caricatures that we usually see?

I have to admit that I actually did not get to include the amount of detail I wanted – I mostly restricted biographical sections to the period a given authority was working on a particular problem or idea – but I thought it was essential to provide some background as to who these people were and why they did what they did. In the case of Lamarck, for example, I didn’t know anything about his life outside of his ideas about evolution before writing the book, so I thought including a little more information about him would be a small way of helping his public image since he is so often trotted out to be a contrast to Darwin and nothing else.

The sources I used varied from figure to figure. For Cuvier, I relied on various historical papers and Martin Rudwick’s selected translations of his work in Georges Cuvier, Fossil Bones, and Geological Catastrophes, whereas I used Adrian Desmond’s biography Huxley and the naturalist’s original research papers for sections about the man famously called “Darwin’s Bulldog.” The most difficult challenge was Charles Darwin. So much has been written about him that I could not possibly read it all, so in addition to biographical accounts I used the Darwin Correspondence Project and The Complete Work of Charles Darwin Online to dig into his original writings as much as possible. Of course my account of Darwin’s work is framed in terms of paleontology – I could not comprehensively cover everything he did, especially since he was such a prolific naturalist and correspondent! – but I tried to hit the major points of his career leading up to 1859 without derailing the paleontological thread of the book.

Finally – what’s next? I know you will be busy traveling the country promoting the book, but I am wondering if you already have the ideas for the next book?

I actually don’t have many travel plans. I’ll be giving a few talks in the NY-NJ-PA area, but I don’t have the budget to allow for a full-scale book tour. I am going to focus on doing what I do best – keeping up my blogs and trying to find more stories to tell in more formal science publications and journals. If opportunities to travel and talk about the book pop up, I’ll jump, but I have no idea when or where such opportunities will arise.

If anything, I have too many ideas for future books. Some are just the seeds of future projects which will require significantly more background than I presently have to cultivate, whereas others I am already in the process of starting. Right now I am trying to choose between two different projects – one on the “Dinosaur Enlightenment” which is rapidly changing our understanding of the charismatic creatures, and another on the controversial idea of “Pleistocene Rewilding.” I fully intend on writing both, but which comes first depends on an array of factors from my ability to travel to places relevant to the books to the willingness of publishers to jump at the projects. Beyond those, I have at least three more ideas for long-term book projects on three disparate subjects, so with any luck I will be writing for some time to come!

And, as a closing note, thank you for your help and support, Bora. You have been behind my writing from the very beginning, and it has been a pleasure to talk to you about a book which has grown directly from my work online. Your ongoing encouragement has helped drive me to become a more professional science writer, so I am genuinely thrilled that you enjoyed the book.

Thank you so much for the interview. And let’s hope that book sells very well – it surely deserves it.

Sigma Xi pizza lunch lecture: Images of Darwin and the Nature of Science

From Sigma Xi:

Join us at noon, Tuesday, Oct. 19 here at Sigma Xi to hear NC State University evolutionary biologist Will Kimler talk about “Images of Darwin and the Nature of Science.” Prof. Kimler researches the history of evolutionary ideas in natural history, ecology, genetics and behavior.

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 cclabby@amsci.org

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

Postscript to Pittendrigh’s Pet Project – Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture Poop

ResearchBlogging.orgPostscript to Pittendrigh's Pet Project - Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture PoopThis is an edited, expanded, updated, revised and (hopefully) improved version of an old post. You can see the original here (or click on the “From The Archives” icon as usual).

Have you ever been out in the country visiting a farm? If so, you must have seen piles of manure, either stashed somewhere or just lying around the paddocks. And if that manure was a little older and starting to dry out and decompose, you likely saw some fine, white fuzz on its surface. Have you seen that? That fuzz is Pilobolus (not the dance troupe, but the fungus), one of a number of species in the genus. If you had a strong magnifying glass with you, and you trained it at the fuzz, you would have seen something like this:

Pilobolus has a portion of its life-cycle in which it has to pass through the digestive tract of a large herbivorous mammal. Since large mammals roam far and wide, this is a great way for the fungus to disperse. There is one problem, though: once excreted out with the feces, how do fungal spores get back into a large mammal again?

Unlike rabbits and some rodents, large mammals do not tend to eat their own manure. Actually, if you observe a field with a properly kept cow herd – a relatively small number of animals in a relatively large area, and rotated regularly between fields – you will notice that all the cows poop in one spot and no cow ever comes close to that spot to graze. So, what is a poor Pilobolus to do?

It gets ready, it aims, and it shoots!

Ready

Pilobolus assumes the position, builds a weapon, fills it with ammunition, aims and shoots. The position is on top of the pile of manure. The ammunition are spores, packaged tightly at the very tip of the filament. The weapon is the sporangiophore, a large swelled organ right below the tip.

The sporangiophore fills up with sap – osmotically active compounds – which builds up pressure until it is about 7 kilograms per square centimeter (100 pounds per square inch). There is also a line of weakness where the cap – the spore package – joins the sporangiophore vesicle. In the end, the pressure causes the sporangiophore to explode which sends the package of spores far, far away – if the wind is in the right direction, as far as 12 feet.

The goo from the sporangiophore goes with the spore package. It is very sticky, so wherever the spores land they tend to stay put. Ideally, that is on a blade of grass which is far enough from the manure pile to have a chance of getting eaten by a cow.

Here is a pretty picture of Pilobolus and a photomicrograph of the spore mass (crushed by the slide and slipcover):


[images from BioImages]

This is very cool (though wait for more coolness below), but also has an economic and environmental impact. Pilobolus spores themselves do not cause harm to their mammalian hosts, but some parasitic worms have evolved a neat trick – hitchiking on the Pilobolus spores right into the digestive tracts of large mammals.

While domestic cattle is regularly dewormed, the real problem is with wild ruminants, especially in places in which they do not have large areas to roam in, as in the elk in the Yellowstone Park. Here is a photograph of a Pilobolus harboring the Dyctiocaulus larvae:

Aim

So, Pilobolus shoots its spores really far away, by exerting enormous pressure on the ‘cap’. But, anyone who’s been in an artillery unit in the military will tell you that the distance is determined by angle. Soldiers manning the cannons know that an approximately 45 degree angle of the cannon will result in the greatest distance for the projectile. But a cannon projectile is a large, heavy object (also smooth and aerodynamic), so air resistance plays almost no part in this calculation – the force of gravity is the only force that the projectile needs to overcome.

A fungal spore is a microscopic object. At the small scale (pdf), physics works a little differently – gravity effects are minimal and the air resistance (drag) is the main determinant of maximal distance. Thus, 45 degrees is not neccessarily the optimal angle for achieving the greatest distance.

Frances Trail and Iffa Gaffoor, working with Steven Vogel at Duke University, made some calculations (which I have not seen and I do not think they got published, but I heard them from Dr.Vogel some years ago), looking at the shape and size of spore-caps of several species of Pilobolus (they published data on some other shooting fungi, though – you can read the paper here if you have access, sorry – not OA). The optimal angle for maximal distance ranges, in different species, between 9 and 30 degrees, the most common fuzz found on cow dung requiring about 15 degrees. The maximal distance, without wind, is about 6-7 feet. Quite right. Six feet is about as close as cows will come to a cowpie in well managed cattle establishments.

But does Pilobolus really shoot at 15 degrees? Well, what it does is it shoots towards the Sun. The way Pilobolus aims is through positive phototaxis. Like a sunflower, it follows the Sun in the sky and shoots at the Sun in the morning.

If you place Pilobolus in a box with light coming in only through a pinhole, all the fungi will shoot their spores at the pinhole:

How does Pilobolus see the light? Beneath the sporangium is a lens-like subsporangial vesicle, with a light-sensitive `retina’. It controls the growth and shape of the sporangiophore quite precisely. Thus, the packet of spores is always aimed at a light source:

So, the Pilobolus spores are found 6-12 feet away from the manure and they reproduce quite nicely even in the best managed cattle herds. So, they are probably shot at their optimal 15-degree angle. But they shoot at the Sun. Ergo, they shoot at the Sun when the Sun is about 15 degrees above the horizon.

One can think of two possible ways this can be achieved. One would be a mechanical sensor that triggers the explosion when the angle between the stalk and the cap is 15 degrees. This would work only if each individual was always standing upright on a flat surface, which is not the case on the rough relief of a manure pile.

The other strategy is to time the release so it coincides with the time when the Sun is about 15 degrees above the horizon. But, the trajectory of the Sun differs at different times of year.
In the middle of the summer in a high latitude, when the daylength is, let’s say, 18 hours, the Sun shoots straight up from the East and reaches the zenith right above exactly at noon. Thus, the Sun is around 15 degrees above the horizon about 90 minutes after dawn.

In winter, when the day may be only 6 hours long, the Sun traverses the sky low above the horizon from East to South to West, and may reach 15 degrees much slower (some Earth scientist in the audience can make a quick calculation here), e.g., 2 or even 3 hours after dawn.

How does the Pilobolus adjust to seasonal differences in Sun’s trajectory? By using its circadian clock, which entrains to different photoperiods with a systematically different phase:

Actually, the Pilobolus was the first fungus in which a clock was discovered. The effects of daylength on timing of spore-release was discovered back in 1948. The endogenous rhythmicity – meaning that the spores get shot every day even if there is no light present (in continous darkness) – was discovered in 1951. The major breakthrough was provided by (pdf) Esther-Ruth Uebelmesser in her dissertation:

At the same time that Schmidle published his findings, Esther-Ruth Uebelmesser (1954) dedicated her thesis work to the same subject. Her thesis is remarkable in many ways. Many of her experiments anticipated circadian protocols, frequently used in later years (different T-cycles and photoperiods, reciprocity, night interruption experiments, entrainment by temperature cycles, etc.). Although she did not fully exploit the richness of her experimental approaches in her interpretations, she must be considered a pioneer of the field and has certainly inspired Colin Pittendrigh to use Pilobolus as a circadian model system (Bruce et al., 1960). Probably, Pittendrigh abandoned this model system because of the unbearable smell penetrating the laboratory when the bovine dung media was prepared (Michael Menaker and Gene Block, personal communication, December 2000).

—————————snip—————————-

While in Neurospora accumulation of conidia (conidial bands) appears to be driven in these protocols with a constant phase angle in reference to lights-off (Fig. 2A), the phase angle of the spore-shooting rhythm in Pilobolus was systematically different with changing cycle lengths (Fig. 2B), possibly reflecting circadian entrainment. Closer investigation, however, revealed that the Pilobolus sporulation rhythm is also driven by the LD cycle, but unlike in Neurospora, by lights-on. Sporulation in Pilobolus is triggered by light, and the spores mature for approximately 28 h before they are shot (see arrows in Fig. 2B and C). The maturation time represents a kind of memory capacity for prior events. This is seen in experiments in which the fungi were released to DD (e.g., from LD 4:4 shown in Fig. 2C). The rhythm, synchronized to a given light cycle, persists for another 28 h until the endogenous circadian control takes over. Thus, depending on conditions, the production of asexual spores in Pilobolus is controlled both by the clock (phase angle) and by light (a driven spore release once per LD cycle).

[images from Roenneberg and Merrow 2001]

What this all means is that a circadian clock in this fungus is entrained by the dawn (not dusk) and it integrates photoperiodic information in a manner that is consistent with the need to shoot spores towards the Sun at the time of the morning when the Sun first reaches 15 degrees (actually, the tracking movement of the spore lags the Sun by about 20 minutes – fungi are slow to move – but even that is probably compensated for by the circadian clock).

Moreover, Pittendrigh’s students discovered that the Pilobolus clock is extremely sensitive to light (both intensity and duration of light). Its clock requires only a millisecond of light to be completely reset.

Shoot

In a more recent paper, the explosive ejection of the spores was filmed with an ultra-high-speed video camera and in their subsequent calculations derived from the images, the “launch speeds ranged from 2 to 25 m s−1 and corresponding accelerations of 20,000 to 180,000 g propelled spores over distances of up to 2.5 meters.” You can see the video (turn on the volume – it is set to music) here:

What next?

This is where the story ends, for the time being. But there are still gaps.

For instance, I am not sure if it was ever tested in the laboratory that Pilobolus actually shoots at 15 degrees. This is, according to Dr.Vogel, relatively easy to do, by placing the fungi on a manure-based medium at the center of one of those transparent semi-spheres used by exhibitors at various product fairs (e.g., technology fairs). The ejected spores stick to the inside of the transparent plastic and can be seen from the outside. Measuring the length of the arc from the desk to the spore (and knowing the radius) is all one needs to calculate the angle.

Second, we still do not know for sure if the Pilobolus cues in to the season-specific photoperiod (more likely) or the season-specific Sun trajectory (less likely). One can, in the laboratory, dissociate these two factors by exposing groups of fungi to summer-specific photoperiod and winter-specific trajectory (using a strong flashlight attached to a string and mounted on an arc-shaped wire, attached to a little motor) or vice-versa, as well as season-specific photoperiod with diffuse (instead of focused) light source.

Finally, an evolutionary question. Horses are not as picky as cows concerning the distance from the manure at which they will graze. Pilobolus lives in our horses and shows up in the manure all the time. Is there relaxed selection for the populations (species?) that live in horses? Is their timing off? Is their angle-determination lousy? This would be an easy head-to-head test in the lab (and field) as well. And if there is such a difference between species, looking at molecules – dynamics of gene expression patterns and protein-protein interactions – can perhaps teach us something more about the ways simple parts can accomplish complex tasks in these organisms.

But, if you’d rather learn all of the above in a Dr.Seuss-like poem, go ahead, it’s right here.

References:

Bruce, V., Weight, F., & Pittendrigh, C. (1960). Resetting the Sporulation Rhythm in Pilobolus with Short Light Flashes of High Intensity Science, 131 (3402), 728-730 DOI: 10.1126/science.131.3402.728

TRAIL, F., GAFFOOR, I., & VOGEL, S. (2005). Ejection mechanics and trajectory of the ascospores of Gibberella zeae (anamorph Fuarium graminearum) Fungal Genetics and Biology, 42 (6), 528-533 DOI: 10.1016/j.fgb.2005.03.008

Fischer, M., Stolze-Rybczynski, J., Cui, Y., & Money, N. (2010). How far and how fast can mushroom spores fly? Physical limits on ballistospore size and discharge distance in the Basidiomycota Fungal Biology, 114 (8), 669-675 DOI: 10.1016/j.funbio.2010.06.002

Roenneberg, T., & Merrow, M. (2001). Seasonality and Photoperiodism in Fungi Journal of Biological Rhythms, 16 (4), 403-414 DOI: 10.1177/074873001129001999

Uebelmesser E-R (1954) Über den endogenen Tagesrhythmus der Sporangienbildung von Pilobolus. Arch Mikrobiol 20:1-33.

Yafetto, L., Carroll, L., Cui, Y., Davis, D., Fischer, M., Henterly, A., Kessler, J., Kilroy, H., Shidler, J., Stolze-Rybczynski, J., Sugawara, Z., & Money, N. (2008). The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi PLoS ONE, 3 (9) DOI: 10.1371/journal.pone.0003237

On the Shoulders of Giants

…but skipping a few generations of ever smaller and smaller Giants in-between.

There will be more….but this pairing so far is awesome 😉

Books: ‘The Poisoner’s Handbook’ by Deborah Blum

Poisoner's Handbook cover.jpgIf you picked up The Poisoner’s Handbook (amazon.com) looking for a fool-proof recipe, I hope you have read the book through and realized at the end that such a thing does not exist: you’ll get busted. If they could figure it all out back in 1930s, can you imagine how much easier they can figure out a case of poisoning today, with modern sensitive techniques? And if you have read the book through, I hope you found it as fascinating as I did. Perhaps you should use your fascination with poisons to do good instead, perhaps become a forensic toxicologist?
My SciBling Deborah Blum (blog, Twitter) has done it again – written a fast-paced page-turner, full of action and intrigue, and with TONS of science in it. It reads like a detective novel. Oh, wait, it is a detective novel. Who said that an author has to invent a fictional detective, an Arsene Lupin or Hercule Poirot or Sherlock Holmes or the Three Investigators? There existed in history real people just like them, including Charles Norris and Alexander Gettler, the heroes of The Poisoner’s Handbook.
Charles Norris was the first Chief Medical Examiner of the City of New York, or at least the first one who was actually qualified for that position which, before him, was a political appointment not requiring any expertise. Norris served in this role from 1918. to 1935. and revolutionized both the position and the science of forensic medicine. Alexander Gettler was one of his first appointees, who served as New York City’s chief toxicologist until 1959.
The two of them used their prominent position to set the new high standards for the profession of a public medical examiner, and also set the new high standards for the scientific research in forensic pathology, including forensic toxicology – the study of the way poisons kill and how to detect it. They affected rules and legislation with their work, they sent clever murderers to the electric chair, and exonerated the innocents who were headed that way due to mistakes of the non-science-based courtroom battles. And in order to do that, they needed to do a lot of their own research during many years of long days and nights in the lab performing meticulous and often gruesome studies of the effects of various substances on animals, people, living and dead tissues and coming up with ever more sensitive and clever methods for detecting as small quantities of the poison as was technically possible at the time.
In the author’s note at the end of the book, Deborah Blum notes that there were many other forensic scientists before, during and after the Norris-Gettner era, and many of them got mentioned in the book or are cited in the EndNotes (which I discovered only once I finished the book – I hate the way publishers do this these days!). But it is also true that Norris and Gettner were the leaders – they used their prominent position and political clout, and their meticulous research defined the high standards for the nascent discipline. In a way, the central importance and prominence of these two men worked well for the book – here we have two interesting characters to like and follow instead of a whole plethora of unfleshed names. And as each chapter focuses on one poisonous substance and one or two notorious cases of its use, it is just like following Holmes and Watson through a series of Sir Arthur Conan Doyle’s stories – the two characters are the connecting thread, and they evolve throughout their lives and throughout the book, case by case.
Apart from being a history of forensic toxicology, the book has several other themes that keep recurring in each chapter, as they chronologically unfold. The book is also a history of 1920/30s New York City, and a history of technology and engineering. Carbon monoxide poisoning? That was the beginning of the car craze. Gas? Everyone cooked and heated with it at the time. Some other poisons were easily found in many over-the-counter products in stores and pharmacies.
Having just read On The Grid, I was also attuned to the discussions of infrastructure of NYC in the early 20th century. How did people transport themselves? Air pollution? Gas? Clean water? Wastewater? All sources of potentially toxic chemicals. How efficient was garbage collection? Not much….thus there were many rats. And rats needed to be controlled. And for that, there was plenty of rat poison to be bought. And rat poison can kill a human as well – inadvertently, as a method for suicide, or as a murder weapon. It is kinda fun to see some of the same infrastructure issues, like garbage disposal and pest extermination in N.Y.City, addressed from different angles in different books – this one, On The Grid, as well as Rats, another fascinating science book that covers New York City engineering, infrastructure and politics of the time. All the threads tie in together….
Another topic addressed in each chapter was Prohibition. One can certainly die of a huge overdose of ethyl alcohol normally found in drinks, but at the time when producing and selling drinks was illegal, people still drank, perhaps even more. And what did they drink? Whatever they could find on the black market – home-made concoctions brewed by unsavory types more interested in profit than the safety of their product. Instead of ethyl, those drinks were mostly made of methyl (wood) alcohol which is much more dangerous in much smaller doses. Prohibition saw a large increase in drinking-related deaths, a fact often loudly pronounced by Norris, leading to the eventual end of Prohibition. Can we apply that thinking to the War On Drugs now?
And the story of Prohibition has another element to it – the importance of regulation. An unregulated substance is potentially dangerous. By solving a number of poisoning cases, and by doing their research on the toxicity of then easily available substances, Norris and Gettner have managed to initiate regulation of a number of toxins, or even their removal from the market altogether. Some substances that were found in everything, even touted as health potions (even radioactive substances!!!) were discovered by forensic toxicologists to be deadly, and were subsequently banned or rigorously controlled. Today we have entire federal agencies dealing with regulation of dangerous chemicals, but in the early 20th century, it was the time of laissez-faire murder, suicide, suffering and death.
Finally, after I finished this fascinating book, I realized it gave me something more: an anchor, or a scaffolding, or a context, for every story about poisons I see now. Now every blog post on Deborah’s blog makes more sense – I can fit it into a body of knowledge and understanding I would not have if I have not read the book. This really goes hand in hand with the recent discussions of #futureofcontext in journalism – see The Future Of Context for starters. The idea is that news stories do not provide enough context for readers who tune into a new topic for the first time. A story that is an update on an ongoing story is not comprehensible without some context, which the news story cannot provide. So now various media organizations are experimenting with ways to provide context for people who are just tuning in. The perfect source of context for a topic is a book, especially now that every book appears to have its own website with links and news and a blog and a Twitter feed and a Facebook page. The book provides context, and all these other things provide updates.
For example, reading Bonobo Handshake may not provide much more context for me about animal behavior and cognition since I already have that context, but it certainly now makes it easier for me to understand the news stories regarding conservation of great apes. And without that book I would never have sufficient background in the recent history of Congo to understand and appreciate this comment thread. ‘On The Grid’ gives me context for all news regarding infrastructure. Explaining Research is a great recent example of a book that is a great start on the topic, but which constantly reminds the reader that this field is in flux and that the book’s website contains frequent updates and additional resources. The Immortal Life of Henrietta Lacks provides fantastic context for the discussions of medical ethics and its evolution in the USA in the past several decades, which I riffed off a little bit in my latest interview.
What reading The Poisoner’s Handbook did for me is to give me enough knowledge and understanding on the topic that I can really appreciate it. I now get excited about news stories regarding poisons because I feel I understand them better. While reading Deborah Blum’s blog was interesting before, now it is more than interesting – it is exciting and I can’t wait for a new post to show up. I did not know how much I did not know. Now that I do, I want to know more. I am hungry for more knowledge, and more news, and more stories about toxins and poisons and how various strange and not so strange substances affect our bodies – where they come from, how they get in, how they hijack or disrupt our normal biochemical processes, how they kill us, and how do we figure that all out in the laboratory or in the basement of the mortuary. I hope you will feel the same once you finish reading this book. You will do that now, OK?