Monday, April 29, 2013

The History of Science: When Was The Word "Scientist" First Used?

As a scientist, I found Prof. Laura Snyder's TED talk fascinating. I suspect her narrative on the history of science will have wide appeal, which is why Im sharing it here as a blog post rather than tweet. 

Prof. Laura Synder is a Fulbright Scholar and Professor of Philosophy at St. John's University. In her talk, she illuminates to me and I suspect to you as well that the word "scientist" was shockingly first used in 1833, not that long ago! We owe its origins to a poet's inquisitiveness. Ultimately, it was the scientist William Whewell who coined the term scientist in response to the poet's plea that "natural philosophers" upgrade the name of their profession. How could it be that the word scientist was invented so recently?

She gives flesh to four Cambridge University students who in 1812 formed the "Philosophical Breakfast Club" to talk about the state of science in Britain and the world. In ushering in a new scientific revolution that even reached to Charles Darwin, the Philosophical Breakfast Club rapturously changed science. She also reminds us loud and clear that "science is not just for scientists". These six words spoken at the end of her talk resonate boldly with me. They are an anthem for science communication and outreach and for social media platforms like Twitter and Blogging that build bridges between scientists and those interested in science.

And for those that prefer reading over watching, here is Laura Snyder's TED talk transposed to text. Ive highlighted in blue some key sections that stand out to me. 

"I'd like you to come back with me for a moment to the 19th century, specifically to June 24, 1833. The British Association for the Advancement of Science is holding its third meeting at the University of Cambridge. It's the first night of the meeting, and a confrontation is about to take place that will change science forever.

An elderly, white-haired man stands up. The members of the Association are shocked to realize that it's the poet Samuel Taylor Coleridge, who hadn't even left his house in years until that day. They're even more shocked by what he says.

"You must stop calling yourselves natural philosophers."

Coleridge felt that true philosophers like himself pondered the cosmos from their armchairs. They were not mucking around in the fossil pits or conducting messy experiments with electrical piles like the members of the British Association.

The crowd grew angry and began to complain loudly. A young Cambridge scholar named William Whewell stood up and quieted the audience. He politely agreed that an appropriate name for the members of the association did not exist.

"If 'philosophers' is taken to be too wide and lofty a term," he said, "then, by analogy with 'artist,' we may form 'scientist.'" This was the first time the word scientist was uttered in public, only 179 years ago.

I first found out about this confrontation when I was in graduate school, and it kind of blew me away. I mean, how could the word scientist not have existed until 1833? What were scientists called before? What had changed to make a new name necessary precisely at that moment? Prior to this meeting, those who studied the natural world were talented amateurs. Think of the country clergyman or squire collecting his beetles or fossils, like Charles Darwin, for example, or, the hired help of a nobleman, like Joseph Priestley, who was the literary companion to the Marquis of Lansdowne when he discovered oxygen. After this, they were scientists, professionals with a particular scientific method, goals, societies and funding.

Much of this revolution can be traced to four men who met at Cambridge University in 1812: Charles Babbage, John Herschel, Richard Jones and William Whewell. These were brilliant, driven men who accomplished amazing things. Charles Babbage, I think known to most TEDsters, invented the first mechanical calculator and the first prototype of a modern computer. John Herschel mapped the stars of the southern hemisphere, and, in his spare time, co-invented photography. I'm sure we could all be that productive without Facebook or Twitter to take up our time. Richard Jones became an important economist who later influenced Karl Marx. And Whewell not only coined the term scientist, as well as the words anode, cathode and ion, but spearheaded international big science with his global research on the tides. In the Cambridge winter of 1812 and 1813, the four met for what they called philosophical breakfasts. They talked about science and the need for a new scientific revolution. They felt science had stagnated since the days of the scientific revolution that had happened in the 17th century. It was time for a new revolution, which they pledged to bring about, and what's so amazing about these guys is, not only did they have these grandiose undergraduate dreams, but they actually carried them out, even beyond their wildest dreams. And I'm going to tell you today about four major changes to science these men made.

About 200 years before, Francis Bacon and then, later, Isaac Newton, had proposed an inductive scientific method. Now that's a method that starts from observations and experiments and moves to generalizations about nature called natural laws, which are always subject to revision or rejection should new evidence arise. However, in 1809, David Ricardo muddied the waters by arguing that the science of economics should use a different, deductive method. The problem was that an influential group at Oxford began arguing that because it worked so well in economics, this deductive method ought to be applied to the natural sciences too. The members of the philosophical breakfast club disagreed. They wrote books and articles promoting inductive method in all the sciences that were widely read by natural philosophers, university students and members of the public. Reading one of Herschel's books was such a watershed moment for Charles Darwin that he would later say, "Scarcely anything in my life made so deep an impression on me. It made me wish to add my might to the accumulated store of natural knowledge." It also shaped Darwin's scientific method, as well as that used by his peers. [Science for the public good]

Previously, it was believed that scientific knowledge ought to be used for the good of the king or queen, or for one's own personal gain. For example, ship captains needed to know information about the tides in order to safely dock at ports. Harbormasters would gather this knowledge and sell it to the ship captains. The philosophical breakfast club changed that, working together. Whewell's worldwide study of the tides resulted in public tide tables and tidal maps that freely provided the harbormasters' knowledge to all ship captains. Herschel helped by making tidal observations off the coast of South Africa, and, as he complained to Whewell, he was knocked off the docks during a violent high tide for his trouble. The four men really helped each other in every way. They also relentlessly lobbied the British government for the money to build Babbage's engines because they believed these engines would have a huge practical impact on society. In the days before pocket calculators, the numbers that most professionals needed -- bankers, insurance agents, ship captains, engineers — were to be found in lookup books like this, filled with tables of figures. These tables were calculated using a fixed procedure over and over by part-time workers known as -- and this is amazing -- computers, but these calculations were really difficult. I mean, this nautical almanac published the lunar differences for every month of the year. Each month required 1,365 calculations, so these tables were filled with mistakes. Babbage's difference engine was the first mechanical calculator devised to accurately compute any of these tables. Two models of his engine were built in the last 20 years by a team from the Science Museum of London using his own plans. This is the one now at the Computer History Museum in California, and it calculates accurately. It actually works. Later, Babbage's analytical engine was the first mechanical computer in the modern sense. It had a separate memory and central processor. It was capable of iteration, conditional branching and parallel processing, and it was programmable using punched cards, an idea Babbage took from Jacquard's loom. Tragically, Babbage's engines never were built in his day because most people thought that non-human computers would have no usefulness for the public. [New scientific institutions]

Founded in Bacon's time, the Royal Society of London was the foremost scientific society in England and even in the rest of the world. By the 19th century, it had become a kind of gentleman's club populated mainly by antiquarians, literary men and the nobility. The members of the philosophical breakfast club helped form a number of new scientific societies, including the British Association. These new societies required that members be active researchers publishing their results. They reinstated the tradition of the Q&A after scientific papers were read, which had been discontinued by the Royal Society as being ungentlemanly. And for the first time, they gave women a foot in the door of science. Members were encouraged to bring their wives, daughters and sisters to the meetings of the British Association, and while the women were expected to attend only the public lectures and the social events like this one, they began to infiltrate the scientific sessions as well. The British Association would later be the first of the major national science organizations in the world to admit women as full members. [External funding for science]

Up to the 19th century, natural philosophers were expected to pay for their own equipment and supplies. Occasionally, there were prizes, such as that given to John Harrison in the 18th century, for solving the so-called longitude problem, but prizes were only given after the fact, when they were given at all. On the advice of the philosophical breakfast club, the British Association began to use the extra money generated by its meetings to give grants for research in astronomy, the tides, fossil fish, shipbuilding, and many other areas. These grants not only allowed less wealthy men to conduct research, but they also encouraged thinking outside the box, rather than just trying to solve one pre-set question. Eventually, the Royal Society and the scientific societies of other countries followed suit, and this has become -- fortunately it's become -- a major part of the scientific landscape today.

So the philosophical breakfast club helped invent the modern scientist. That's the heroic part of their story. There's a flip side as well. They did not foresee at least one consequence of their revolution. They would have been deeply dismayed by today's disjunction between science and the rest of culture. It's shocking to realize that only 28 percent of American adults have even a very basic level of science literacy, and this was tested by asking simple questions like, "Did humans and dinosaurs inhabit the Earth at the same time?" and "What proportion of the Earth is covered in water?" Once scientists became members of a professional group, they were slowly walled off from the rest of us. This is the unintended consequence of the revolution that started with our four friends.

Charles Darwin said, "I sometimes think that general and popular treatises are almost as important for the progress of science as original work." In fact, "Origin of Species" was written for a general and popular audience, and was widely read when it first appeared. Darwin knew what we seem to have forgotten, that science is not only for scientists."

Thank you.

Via Source

Thursday, April 25, 2013

Social Media for Scientists: YouTube One Channel

If you have videos posted to youtube, then you should definitely check out the new layout design. In the span of ten minutes, you can customize your "YouTube One Channel" as they now call it with a banner from your gallery or theirs, feature video, and a list of videos that you can customize according to theme, recency, popularity, etc. If you do not post videos to youtube, then you should. Its a great way to give wings to your science to other scientists and the public. Consider it a broader impact if you will. Video pages are on the rise, like twitter and facebook. They are here to stay as an online footprint of your life or profession, whatever you may choose. For scientists or educators, lectures, seminars, news features, TED talks, etc are all great things to post. Ive gotten immense benefit from watching research seminars on youtube because there are always meetings that you miss or talks you would like to hear twice. If you set up a channel, let me know so I can subscribe to it!

The Microbiome Blurs the Lines Between Genes and Environment

On the lecture circuit this past couple of months, Ive given talks about the hologenome (link to video post), which is the term being used by 
From Wikicommons
some to refer to the collection of eukaryotic cells and microbial cells that make up the organism. By far, the most common and intriguing question I get is whether the microbiome is a (i) phenotype, (ii) genotype, or the (iii) environment. Quite honestly, its more complicated than you might think at first. Genes involved in immunity select for the presence of certain microbes, making the microbiome almost like a phenotype that is encoded for. Microbes are also genotypes themselves with their genomes providing life-serving functions that our genome does not encode for. Finally, microbes are in and part of the external environment, and the nuclear genome could live with a microbiome much like the organism lives with a certain ph or moisture. This question is a rabbit hole that we can go deep into. To my surprise, Science 2.0 just recently posted this excellent article below on the very issue raised here. It's well worth a read, a nap, and then another read. Then read the comments section as well. What do you think? As always, I welcome your thoughts on how far down the rabbit hole we can go.

Natural Selection And Microbiota
By Gerhard Adam | April 16th 2013 01:00 AM | 7 comments | Print | E-mail | Track Comments
There is no question that Darwin's tremendous insight into the mechanisms by which evolution occurred was one of the singularly most significant events in biology.  Similarly with the discovery of DNA and genetics, the processes by which organisms were formed received a similar boost.  So the purpose of this article is not to argue that Darwin or genetics is wrong.  Instead, the point is to suggest that it is necessarily incomplete.  In the same way that Darwin's work was incomplete because he lacked the necessary information about genetics.  The modern evolutionary synthesis is also incomplete, because it fails to extend the issues of natural selection in an organism's development to their co-evolutionary partners; the microbes.

"Evolution is cleverer than you are" Orgel's rule.

Nowhere does this ring more true than in examining the incompleteness of what we understand about the process of life perpetuating itself.

Naive group selection gave rise to gene-centricism, from which we acquired kin selection and inclusive fitness theories.  Every one of which takes an essentially linear view of natural selection.  Parents pass on their genes to offspring, which are selected for, in turn passing on their traits.  The gene is considered the unit of selection, so that it is characterized, metaphorically, as being "selfish" in its interest of having greater representation in future generations.  Behavioral traits, such as cooperation and altruism, are explained by suggesting that we benefit by assisting other genes to be passed into future generations, as long as we are related in some fashion.  As a result, there is a supposed genetic explanation for every permutation of traits that exists, even those that have zero biological fitness.  Hopefully an alternative view may offer a different perspective on such thinking.

This all presents a nice concise package, except that it isn't the full story and it may not even be fully true.

In the first place, we have to recognize that this entire story presumes a level of biological isolation that simply doesn't exist.  Every organism must cope with the environment that it exists in, while simultaneously serving as an environment for many other creatures.  Each exerts an influence on its environment, as well as the environment exerting influences in return.

There is no isolation.

Therefore, one of the first problems we encounter is the notion that the gene is the unit of selection.  Certainly recent work in epigenetics has demonstrated that there are other influences that can determine whether a gene is expressed or not, so it is clear that the gene cannot singularly be responsible for the traits an organism exhibits, if it can't actually ensure that it is expressed, or how it is expressed. Moreover, the concept of "selfishness" is demonstrably wrong because every instance where such behavior manifests, results in the destruction of the organism (segregator distorter genes, carcinomas, etc.).  Therefore, we should dispense with the notion of the gene being the singular unit of selection, and simply concede that it is a means of selection.  In other words, it simply carries the "message" which may be utilized or ignored as determined by other processes.

This has already largely been recognized, since genetic expression may be influenced by environmental factors, but nevertheless, the persistent view that the genes are the "blueprint"pervades most views of evolution.  There is no question that the gene is the means by which information is replicated and passed between generations.  That isn't in dispute.  However, this is only one stage of a multi-stage operation that will ultimately result in a viable organism that is capable of competing and whose fitness will determine "success" or "failure".

However, we have some new insights to consider and they are quite radical.  In the first place, we are not the "owners" of our bodies.  We are outnumbered in our own bodies, by microbes by a ratio of over 10 to 1.  The genomes represented by these microbes outnumbers our own by 100 to 1.  

In studying germ-free (GF) mice we can now see that genes are insufficient to produce a viable organism.  Of course, there have already been strong hints of that in many other animal species.  After all, what does it mean to produce a termite genetically, if one doesn't account for the symbiotic protozoans necessary to digest its food?  There are many other such relationships, that are conveniently termed symbiotic, but in truth represent absolutely essential traits on which the creature has evolved to depend on.

Therefore, one of the first conditions we must recognize is that we do not evolve alone, nor does natural selection work solely on the products of our genes.  We are dependent on our microbes for survival and selection as they are on us for their environment.

Moreover, these microbes can't just be arbitrarily introduced whenever we choose.  They are specific to individual species and even individuals within a species and must be present/introduced at critical stages of development (1).  This indicates that these microbes aren't merely some external presence that exerts an influence (2).  They are part of the process, as inextricably linked to our development as are the regulatory signals to our own cells.  Even something that is so fundamentally related to fitness, such as pregnancy, requires the involvement of microbes for success.

[NOTE:  It also doesn't appear that there is any particular uniformity of microbes to any individual beyond providing assistance in similar metabolic ways]

Failure to adhere to these developmental requirements, produces difficulty for the organism in question.

Similarly one has to consider the role of these commensal organisms and their influence on an organism's genes, because if an organism can exploit a trait that already exists, then it reduces or even eliminates the selection pressure for such a trait to be manifest in the genome.

As a result, there are traits that exist for which the genome has no "knowledge".

This raises the question of how much of our survival and response to natural selection is due to micro-organisms stepping into the breach to provide a critical service for which our genome was unprepared?  

Whatever else we may think, it is clear that viewing an organism and natural selection, from the pureperspective of genes is incomplete (3).  Therefore it may be more precise to say that genes provide the basic environment, while microbes manipulate and refine to produce a working ecosystem.  As a result, as goes their success, so goes our.  

Of course, it is too simple to begin thinking that these microbes are the "heroes" of our scenario, since it is equally important to note that many of the diseases that humans experience are equally the result of such microbes (4).  No matter how one wishes to view this; "friend or foe", the truth is that we're all in this together.

Additional references:

A study by Chung's co-author Kasper showed that mice that were raised germ-free could have their immune systems "rescued" by certain microbes up to the first several weeks of age.

A lot of the medical conditions the microbiome is being implicated in are puzzling. They seem to run in families, but no one can track down the genes involved. This may be because the effects are subtly spread between many different genes. But it may also be that some—maybe a fair few—of those genes are not to be found in the human genome at all.


(4)  Even traditional ideas about what constitutes pathogens may require some revision.


Steve Davis
"This all presents a nice concise package, (ie, the gene-centric interpretation of evolution) except that it isn't the full story and it may not even be fully true."
Gerhard, you are far too kind and gentlemanly! :)
I think the realistic version of the contribution of gene-centrism to evolution is that it is of no value at all.
After all, what can it predict?
One thing only, that the genes of fitter organisms will tend to spread in a population.
And that was put first by Fisher, who did not link it directly to evolution, but to natural selection.
Those two concepts are not the same despite the misunderstanding of gene-centrics.
And the prediction is essentially a truism - it is not an explantion of evolution.
Interestingly, Fisher was smart enough to not throw selfishness into his account - he was a numbers man.
Apart from that, a great article! :)

Gerhard Adam
Thanks ... I'm glad you finally got to make a comment :)

John Hasenkam
If I ever hear another libertarian tell me the "common good" is purely a human moral construct they can go dip their eye in hot cocky's cack ...

Genetic Circuit Allows Both Individual Freedom, Collective Good

Steve Davis
John, that's an interesting article.It brings to mind the view of the greatly under-appreciated Robert Ardrey, that the fittest groups are those that cater for both individual diversity and the stability that comes from social conformity.
Gerhard, you've raised subjects here that are covered in detail in Tom Wakeford's Liaisons of Life, a great read.

Gerhard Adam
Sounds like a good book.

What I find fascinating is examining natural selection's "blind spots".  In other words, if a particular function is provided by a microbe, then there is no selection pressure on the genome and consequently the entire organism is being selected for a trait that it can't even provide by itself [i.e. the microbe does it].

This raises all kinds of interesting questions about how often this type of thing might occur and how deep some of these ramifications may run.

Steve Davis
 "...if a particular function is provided by a microbe, then there is no selection pressure on the genome and consequently the entire organism is being selected for a trait that it can't even provide by itself."
 Ah, but Gerhard, that was explained by RD in The Extended Phenotype - the function is carried out by the microbe on instructions from the host genes!! Were you not paying attention? :)
The power of delusion is great.

Gerhard Adam
Ahh, but that's the interesting part, because it really appears to be the other way around.

Sunday, April 21, 2013

My talk at the University of Indiana at Bloomington

I had the pleasure of visiting The University of Indiana at Bloomington in early April. With nearly 80 biologists sprinkled across the integrative department including many good friends and tweeters, Bloomington is an intellectual hub of life sciences research.

Here's my seminar "Mainlining the Hologenome into Biology". The term hologenome is rather new to biology and some may consider it controversial, even jargon. Part of me concedes that it could be, but a rising number of biologists think that we do need a term like it, i.e., holobiont or metaorganism. For an intro to the origin of the concept, the New Scientist recently featured the hologenome theory on their cover. The future of biology continues to be integrative where the lines between disparate disciplines are increasingly blurry. The term hologenome is useful because it encompasses the rather simple idea that the total microbiome of a host plus its nuclear and cytoplasmic genomes comprise a unit of selection from which nature picks the fittest organism / hologenome. This concept melds the diverse vantage points of evolutionary geneticists and microbiologists; hence, it will not be accepted immediately, nor should it. Big ideas demand big evidence. Further, terms will not change knowledge, but they help to fashion the framework of experimentation that will.

Disclaimer: exuberant editing on the quote slide done in iMovie.

Thursday, April 18, 2013

Microbiome: Can A Fecal Transplant Cure Autism?

Bar chart showing autism diagnosis increase in the U.S. from 1996 through 2005.CC-BY-SA-3.0 (],
via Wikimedia Commons

Studies of the microbes and their genes, which we collectively term the Microbiome, have been performed for many chronic illnesses including Autism. There is considerable and recent attention on this issue, but thus far, scientists have shown potential correlations between autistic patients and shifts in their microbiome. Nothing conclusive and other studies do not find the same correlations. There's even a documentary on the topic called the Autism Enigma that perhaps oversells the idea that the microbiome is the cause of autism.

News links:
Open Access Papers:
While I'd like to hope that something as enigmatic as Austism has a microbial, and therefore potentially, curable basis, I was disappointed to find a chat on line where a fecal transplant had been performed to transplant healthy poop/microbes into the gut of an Autistic child. Unfortunately, weeks of monitoring after the fecal transplant did not appear to significantly affect the symptoms of that child. Its a sample size of 1, so take it with a grain of salt. But in this case, the fecal transplant did not cure Autism behaviors.
However, minor OCD with fans and holding/twiddling 2 of the same item remains.
The transplant did seem to stabilize gut symptoms:
At the 3 1/2 week mark, still no bacteria flares or yeast flares, all with no antimicrobials and just 1 culturelle a day. Bowel movements are still really good with no diarrhea or blow outs. Appetite is nice too. Weight is steady with maybe a slow increase.
I've previously written about the powerful affects that fecal transplants have on IBD, IBS, C. diff, Colitis and perhaps Multiple Sclerosis.

If anyone has any other information on how probiotics, prebiotics, or stool transplants work for Autism,  do share them here to spread the word around.

As always, thanks for reading and sharing your opinions.