Creationists are fond of mentioning people who are committed to creationism but still function as successful scientists. We saw an example in the debate between Bill Nye and Ken Ham. These creationist "scientists" are often physicians or engineers.
It seems obvious to most of us that engineers and physicians are not scientists. PZ Myers mentions this on his blog when he discusses the debate as reviewed by William Saletan: Saletan is at it again. Here's what PZ says ...
Engineers can practice real science, but an engineer is not the same thing as a scientist. I agree that creationists can be perfectly good engineers, but how can you trust the scientific acumen of someone who insists that the earth is only 6,000 years old? That says right there that they have no respect for the evidence. How can Saletan ignore Ham’s bogus distinction between historical and observational science, in which he flatly rejects any possibility of inference about the past from the present? This creationism is utterly incompatible with biology, anthropology, geology, astronomy, climate science, geochemistry, cosmology, and any other science that deals with cause and effect and history. These sciences apparently do not matter to Saletan, as long as engineers make satellites and doctors do surgery.
Saletan cites Ham’s videos as falsifying the claim that creationism is incompatible with science. Ken Ham makes a big deal of this, too.
This would be unremarkable except that Jason Rosenhouse disagrees [Saletan vs. Myers on Nye vs. Ham]. Here's what Jason says ...
Oh for heaven’s sake! Engineers are scientists. Full stop. Are you really that desperate to deny that a creationist could ever make a contribution to science that you will sink to this level of insult and idiocy? (Yes, it is insulting to suggest that engineers are not scientists.)
Engineers have a Bachelor's degree in engineering and they typically work for a construction company or in the IT department of a large corporation. They are not scientists. Full stop.
It's true that some engineers do science but usually they have a higher degree in engineering and usually they are academics. There's no possible way you could assume that all engineers are scientists just because they are licensed engineers and wear the ring. I'm sorry, Jason, but you are wrong.
Similarly, the typical physician has a private practice at a strip mall in the suburbs. They have an M.D. degree that can be earned right out of high school (in Europe). They are not scientists.
There are some physicians who are scientists and some of them have earned Nobel Prizes. They are the exceptions, not the rule. It's ridiculous to assume that everyone with an M.D. is a scientist.
There's a big difference between publishing the complete sequence of a genome and having a highly accurate "finished" version that's fully annotated. You may be surprised to learn that there aren't very many high quality genomes of eukaryotes—especially vertebrates.
That's why I was interested in a paper published last April on the zebrafish genome. The authors have produced a high quality reference genome that will serve the scientific community (Howe et al. 2013).
Sequencing and assembly are highly automated and there are several programs that will find genes and other interesting bits of a draft genome. It's a lot more work to finish off the sequence by filling the gaps and it's even more work to annotate and check the sequences. Much of this work is labor intensive and expensive and that's why there are so many unfinished sequences in the literature.
I wasn't surprised to see that the original paper on the annotated zebrafish genome had 171 authors although that did seem a bit excessive. It meant that each author contributed an average of 0.6% to the final result. Some of them must have made a much smaller contribution. I wonder if every author read and approved the paper before publication?
Apparently there weren't enough authors. The January 9, 2014 edition of Nature contains a Corrigendum (correction) to the zebrafish paper. Five other authors were "inadvertantly ommitted" from the list bringing the total to 176 authors. In addition, the names of three other authors were spelled incorrectly in the original publication last April. I don't know why it took eight months before anyone noticed.
That just goes to show you that modern scientists have to deal with problems that us old fogies never encountered. I never had to spent more that a few seconds writing down the names of the authors on any of my papers. Today you need data management software to keep track of your authors.
Howe, K. and 171+5 others (2013 The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498–503. [doi: 10.1038/nature12111]
The Clergy Letter Project is sponsoring the 9th annual "Evolution Weekend" on February 7-0 2014. This is a weekend where clergy talk to their congregations about science and evolution. Here's how they describe the event ...
Evolution Weekend is an opportunity for serious discussion and reflection on the relationship between religion and science. An ongoing goal has been to elevate the quality of the discussion on this critical topic, and to show that religion and science are not adversaries. Rather, they look at the natural world from quite different perspectives and ask, and answer, different questions.
Maybe it's just me, but I thought that "serious discussion and reflection" means that all aspects of the conflict between science and religion would be considered. This includes the possibility that the conflict is very real and cannot be accommodated.
I was wrong. If you are a member of the Clergy Letter Project your mind is already made up.
Because religion and science use different methodologies to understand the world, and because religion and science ask very different questions, there is no reason to view them in conflict. One important facet of Evolution Weekend 2014, therefore, is to explore the questions each ask and to examine the different ways of knowing embodied in each.
There's not going to be any serious discussion about different ways of knowing and which ones are successful.
One of the most important lessons of science is that life evolved from simple primitive organisms over a period of at least three billion years. The history of life can be fully explained by natural causes without any need for miracles or divine intervention. We have learned that the evolution of life on this insignificant planet, in an ordinary galaxy, in a vast universe, has no purpose or goal.
There aren't many religions that can accommodate those facts.
I recently had a discussion about the safety of food derived from genetically modified organisms. My opponent, whose identity I will conceal (hi Rachel!), argued that GM foods are unsafe and that there's scientific evidence to back this up. Naturally, this evidence is being concealed by Monsanto and other private companies in the same way that tobacco companies tried to hide the evidence that smoking causes lung cancer.
My position is that I'm not aware of any reliable scientific studies showing that GM foods are dangerous to your health and, furthermore, in a free and open democracy with a free press it seems highly unlikely that such evidence is being suppressed. It seems even more unlikely that scientists would be part of this conspiracy.
Do you remember Vincent Joseph Torley (vjtorley)? He's the IDiot with a Ph.D. (2007) from the Department of Philosophy at the University of Melbourne (Australia). That's a legitimate university. Apparently Vincent Torley went off the rails sometime after 2007.
The scientific enterprise stands or falls on the legitimacy of making inductive inferences, from cases of which we have experience to cases of which we have no experience. The aim of this post will be to show that there can be no scientific knowledge if there is no God, and that there is no way of justifying inductive inference on a systematic basis, in the absence of God.
BLAH, BLAH, BLAH, etc. etc. etc.
I alluded above to the troubling fact that even if we assume that objects somehow instantiate rules, there remains the epistemic problem of knowing whether we’ve chosen the right model, or identified the right mathematical equation (i.e. laws of Nature) for characterizing the rules that define a certain kind of object – be it a tiny electron or a star, like the sun. But if we make the two assumptions about God which I referred to in the preceding section – that God wants to make intelligent beings, and that God wants these intelligent beings to reason their way to God’s existence – then we can infer that the rules which are embodied by objects in the natural world must be tailor-made to fit the minds of intelligent beings that are capable of contemplating their Creator. In other words, the universe is designed to be knowable by us. Hence we don’t need to concern ourselves with the theoretical possibility that the rules which characterize things might be too complicated even in principle for us to grasp.
God, then, is the ultimate Guarantor that science can work.
Well, that does it for me. Either I stop being a scientist or I have to become a believer in God in order to continue doing science.
Tough choice. Let me get back to you on that one ... anyone want a job as a professor of biochemistry?
The Green Party of Canada is led by Elizabeth May who has a seat in parliament. The Green Party (of Canada) advocates many positions that are anti-science [Do Not Vote for the Anti-Science Green Party].
The article was written by Tristin Hopper. Here's what he says in the opening paragraphs.
Two months ago in Halifax, Green Party leader Elizabeth May appeared at a Stand Up For Science rally; one of many demonstrations held across the country to protest, among other things, a Canada-wide “muzzling” of government scientists.
“You may not like the opinions you get from science, but you have to listen to science,” Ms. May told Halifax radio.
Only a week before, however, Ms. May had been at a town hall meeting in her Saanich, B.C. riding telling her constituents not to trust federal science — albeit from a different agency than the ones being defended on the streets of Halifax.
“Agriculture Canada is increasingly a corporate model for profits, for Monsanto and Cargill, and certainly not to help farmers and certainly not to ensure safe food for Canadians,” said Ms. May.
The point needs emphasis. There's really no serious scientific debate over the safety of GM food. It is safe to eat. That does not mean that every single scientific paper that has ever been published proves that GM food is safe. You can always find some paper somewhere that backs up your preferred view of a scientific issue. Most Sandwalk readers know that real science is determined by the consensus views of the experts in the field and not by the rogue scientists who disagree. If you've been reading my blog, you will also know that in any debate that involves science both sides have to appear to have science on their side because, if you don't have science on your side in the 21st century, you've lost the debate.
Here's how Michael Kruse puts it. (He is quoted in the National Post article.)
“I really think the Green Party is just doing the same things everybody else does, which is to make up an idea that matches with your ideology, and then go looking for evidence to support it,” said Michael Kruse, chair of Bad Science Watch, a non-profit devoted to rooting out false science in public policy.
Michael has it right. The Green Party is doing exactly what a long list of groups do when their favorite beliefs aren't supported by the scientific consensus. They cherry-pick. Then they make up conspiracy theories to explain why climatologists, evolutionary biologists, nutritional scientists etc. are misleading the general public about the real science in their field.
In a July essay, Aaron Larsen, a Canadian-born Harvard post-doctoral fellow publicly called out the Green Party—his preferred choice at the ballot box—for its platform declaring that genetically-engineered crops are a “potentially serious threat to human health and the health of natural ecosystems.”
“Just to be clear, there has never been a single reputable, peer-reviewed study that has found any link between the consumption of genetically modified foods and adverse health effects,” he wrote.
That's why the Green Party is anti-science. There are many other examples of Green Party policies that are anti-science. You should not vote for the Green Party if you value science. I hate to think what might happen to science if it ever became the governing party of Canada.
Christian de Duve died last May. He was the man who discovered peroxisomes and he did important work on other cell compartments such as lysozomes. He was awarded the Nobel Prize in Physiology or Medicine in 1974 but, unfortunately, his name is not as widely recognized as it should be.
I met him a few times when he was working on his book "Blueprint for a Cell" and his second book, "Vital Dust." These books explore a unique perspective on the origin of life and they should be consulted by anyone who is interested in that topic.
You'll also learn how a Belgian gentleman can behave in a way that we in North America cannot yet copy. Perhaps in a few years our countries will also become civilized.
Dr. Christian de Duve remained active until the very end of his life, as this photograph taken in his last year demonstrates. He finished his last book Sept vies en une: Mémoires d'un Prix Nobel only a few months before he passed away. When he felt that both his health and strength were rapidly subsiding, he decided to end his life at the age of 95. He chose to die by an act of euthanasia, while surrounded by his children.
The University of Toronto is sponsoring a "science" festival with three talks tomorrow and Saturday. You have to buy tickets at: tickets.
There's two technology talks and one science talk. I'm going to the only science talk at the science festival. There are a bunch of other things going on, see the entire program.
Friday, Sept. 27th 7pm– "Human Exploration of Space: 50 Years and Counting": Space Shuttle veteran and first Canadian on board the International Space Station, Julie Payette
“High achiever” barely begins to describe Julie Payette. Masters degree in engineering, pilot, IBM engineer, Officer of the Order of Canada, singer with symphonies in Montreal, Toronto, and Switzerland, conversant in six languages, and now Director of the Montreal Science Centre. Oh, did we mention she was orbiting the Earth, using a giant robot arm to build a space station by the time she was 35? Julie will kick off the festival by sharing her unique insights into the past, present, and future of human space exploration.
Friday, Sept. 27th 8pm– "Brave Genius: Jacques Monod, Chance, and our Place in the Universe": Evolutionary biologist and “evo devo” pioneer, Sean Carroll
Biologist and Nobel Laureate Jacques Monod once remarked that “the most important results of science have been to change the relationship of man to the universe, or the way he sees himself in the universe.” Discoveries in molecular biology, evolutionary biology, and geology over the past half-century have profoundly reshaped our picture of human origins, and revealed the enormous role of chance in the fate of life on Earth. Join evolutionary biologist Sean Carroll as he chronicles some of those discoveries through Monod’s eyes, whose own ascent from struggling graduate student to leader within the French Resistance, co-founder of molecular biology, and emergence as a public figure and leading voice of science involved a great deal of chance, and courage.
Saturday, Sept. 28th 7pm– "Postcards from Mars": Mars rover imaging scientist, Jim Bell
Don’t worry if your application to live on Mars was rejected. You can still visit the Red Planet through the spectacular imagery captured by a trio of Mars Rovers—Spirit, Opportunity and Curiosity. Planetary scientist Jim Bell was instrumental in developing cameras and processing images from the three robotic explorers and in his talk “Postcards from Mars”, he’ll share his favorite vistas of our planetary neighbour with you. Through the beauty of these photographs, you’ll see why Bell can be described as a scientist, an explorer and a nature photographer.
One of the criticisms of science (narrow definition) is that its reductionist approach is simplistic and materialistic. Here's how Jesus and Mo dealt with that issue last month.
I'm about to start teaching my course on "Scientific Misconceptions" and one of the most important issues is defining science and dealing with the demarcation problem. Vincent Joseph Torley is also interested in this question—for a different reason—and he discovered an 1945 essay by George Orwell (Eric Arthur Blair (1903-1950)).
It's worth quoting the relevant passages. Doublethink means the power of holding two contradictory beliefs in one's mind simultaneously and accepting both of them. George Orwell
In last week’s Tribune, there was an interesting letter from Mr. J. Stewart Cook, in which he suggested that the best way of avoiding the danger of a “scientific hierarchy” would be to see to it that every member of the general public was, as far as possible, scientifically educated. At the same time, scientists should be brought out of their isolation and encouraged to take a greater part in politics and administration.
As a general statement, I think most of us would agree with this, but I notice that, as usual, Mr. Cook does not define Science, and merely implies in passing that it means certain exact sciences whose experiments can be made under laboratory conditions. Thus, adult education tends “to neglect scientific studies in favour of literary, economic and social subjects”, economics and sociology not being regarded as branches of Science, apparently. This point is of great importance. For the word Science is at present used in at least two meanings, and the whole question of scientific education is obscured by the current tendency to dodge from one meaning to the other.
Science is generally taken as meaning either (a) the exact sciences, such as chemistry, physics, etc., or (b) a method of thought which obtains verifiable results by reasoning logically from observed fact.
If you ask any scientist, or indeed almost any educated person, “What is Science?” you are likely to get an answer approximating to (b). In everyday life, however, both in speaking and in writing, when people say “Science” they mean (a). Science means something that happens in a laboratory: the very word calls up a picture of graphs, test-tubes, balances, Bunsen burners, microscopes. A biologist, and astronomer, perhaps a psychologist or a mathematician is described as a “man of Science”: no one would think of applying this term to a statesman, a poet, a journalist or even a philosopher. And those who tell us that the young must be scientifically educated mean, almost invariably, that they should be taught more about radioactivity, or the stars, or the physiology or their own bodies, rather than that they should be taught to think more exactly.
Every war when it comes, or before it comes, is represented not as a war but as an act of self-defense against a homicidal maniac. George OrwellI agree with Orwell when he prefers the broad definition of science. I see it as a way of knowing that can be applied to any discipline. I think that everyone should become more scientifically literate but by that I don't mean they should lean more about metabolic pathways or quantum chromodynamics. I mean that they should become more familiar with the scientific approach to acquiring knowledge. That's the fundamental skill that we need to learn.
Clearly, scientific education ought to mean the implanting of a rational, sceptical, experimental habit of mind. It ought to mean acquiring a method – a method that can be used on any problem that one meets – and not simply piling up a lot of facts. Put it in those words, and the apologist of scientific education will usually agree. Press him further, ask him to particularise, and somehow it always turns out that scientific education means more attention to the sciences, in other words – more facts. The idea that Science means a way of looking at the world, and not simply a body of knowledge, is in practice strongly resisted. I think sheer professional jealousy is part of the reason for this. For if Science is simply a method or an attitude, so that anyone whose thought-processes are sufficiently rational can in some sense be described as a scientist – what then becomes of the enormous prestige now enjoyed by the chemist, the physicist, etc. and his claim to be somehow wiser than the rest of us?
A hundred years ago, Charles Kingsley described Science as “making nasty smells in a laboratory”. A year or two ago a young industrial chemist informed me, smugly, that he “could not see what was the use of poetry”. So the pendulum swings to and fro, but it does not seem to me that one attitude is any better than the other. At the moment, Science is on the upgrade, and so we hear, quite rightly, the claim that the masses should be scientifically educated: we do not hear, as we ought, the counter-claim that the scientists themselves would benefit by a little education. Just before writing this, I saw in an American magazine the statement that a number of British and American physicists refused from the start to do research on the atomic bomb, well knowing what use would be made of it. Here you have a group of sane men in the middle of a world of lunatics. And though no names were published, I think it would be a safe guess that all of them were people with some kind of general cultural background, some acquaintance with history or literature or the arts – in short, people whose interests were not, in the current sense of the word, purely scientific.
Where did the George Orwells of this world go? Why don't we have more people like him today? Have they just been drowned out by idiots with access to a microphone?
John Mattick and Jonathan Wells both believe that most of the DNA in our genome is functional. They do not believe that most of it is junk.
John Mattick and Jonathan Wells use the same arguments in defense of their position and they quote one another. Both of them misrepresent the history of the junk DNA debate and both of them use an incorrect version of the Central Dogma of Molecular Biology to make a case for the stupidity of scientists. Neither of them understand the basic biochemistry of DNA binding proteins leading them to misinterpret low level transcription as functional. Jonathan Wells and John Mattick ignore much of the scientific evidence in favor of junk DNA. They don't understand the significance of the so-called "C-Value Paradox" and they don't understand genetic load. Both of them claim that junk DNA is based on ignorance.
Dan Graur has a recent post on the phylogeny of placental mammals [The Root of the Placental Phylogenetic Tree: Are we Overlooking Something?]. He refers to a recent review in Molecular Biology and Evolution (MBE) that discusses various options. Graur believes that the question has been settled by examining transposon insertions.
But that's not the part that caught my attention. At the end of his post he says,
Finally, there is a small sentence in the Teeling and Hedges commentary that drove me up the wall: “The timing of the splitting event—approximately 100 Ma based on molecular clocks—is not in debate, at least among molecular evolutionists (Hedges et al. 1996…” Actually, dear Blair, it is. And whether you like it or not, both William Martin and I are fine molecular evolutionists.
The reference is to a paper by Dan Graur and Bill Martin—a formidable team that you want on your side because the alternative can be very embarrassing. You really, really don't want to mess with these guys.
We need more papers like this one.
Graur, D. & Martin, W. (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. TRENDS in Genetics 20:80-86 [doi: 10.1016/j.tig.2003.12.003] [PDF]
One of my ancestors is Katherine de Roet (1349-1403) better known as Katherine Swynford since she married Hugh Swynford. Katherine was the mistress (later wife) of John of Gaunt (1340-1399) and they had several children. I descend from one of them, John Beaufort (1373-1410).1
Katherine's father was Paon de Roet better known as Sir Gilles. He comes from Hainault in Belgium and he served Philippa of Hainault who became the wife of King Edward III of England.
Katherine's sister, also called Philippa (1346-1387) [Philippa Roet] was a prominent member of Queen Philippa's court in England. At first, she was a child companion of the children of Elizabeth of Ulster and the Queen but later on she was a lady-in-waiting. Geoffrey Chaucer became a page in the household of Elizabeth of Ulster in 1357 when he was 14 and Phillipa was 11.
Queen Philippa encouraged them to marry in September 1366. Chaucer and Philippa Roet had two sons and two daughters. The youngest son, Lewis, was born in 1381 and attended Oxford beginning in 1391. Chaucer noticed that his son was interested in science and he wrote A Treatise on the Astrolabe to explain the workings of an astrolabe that he gave him when he was about 10 years old.
A Treatise on the Astrolabe Geoffrey Chaucer
Lyte Lowys my sone, I aperceyve wel by certeyne evydences thyn abilite to lerne sciences touching nombres and proporciouns; and as wel considre I thy besy praier in special to lerne the tretys of the Astrelabie. Than for as moche as a philosofre saith, "he wrappith him in his frend, that condescendith to the rightfulle praiers of his frend," therfore have I yeven the a suffisant Astrolabie as for oure orizonte, compowned after the latitude of Oxenforde; upon which, by mediacioun of this litel tretys, I purpose to teche the a certein nombre of conclusions aperteynyng to the same instrument.
[Little Lewis my son, I perceive well by certain evidences thine ability to learn sciences touching numbers and proportions; and as well consider I thy constant prayer in special to learn the treatise of the Astrolabe. Than for as much as a philosopher saith, "He wrappth him in his friend, that condescendth to the rightful prayers of his friend", therefore have I given thee a suffisant Astrolabe as for our horizons, compounded after the latitude of Oxford; upon which, by means of this little treatise, I purpose to teach thee a certain number of conclusions pertaining to the same instrument.
1. Almost everyone who has European ancestors will eventually connect to European nobility so there are millions of people who descend from John of Gaunt [see Are You a Descendant of Charlemagne?]. If you know the names of all sixteen of your great-great-grandparents and their dates and places of birth, then chances are high that you can make the connection with only a little effort.
Sixty years ago on this day, Nature published three back-to-back papers on the structure of DNA. It was a momentous day for science. Here's how Horace Judson describes it in The Eighth Day of Creations (pp. 154-155)...
The letter to Nature appeared in the April 25 issue. [It was submitted on April 2—LAM] To those of its readers who were close to the questions, and who had not already heard the news, the letter must come off like a string of depth charges in a column sea. "We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest," the letter began; at the end, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." That last sentence has been called one of the most coy statements in the literature of science. According to Watson, Crick wrote it. Wilkins's paper followed, signed also by two of his associates at King's College, A. R. Stokes and H. R. Wilson. It was a restatement of helical diffraction theory, and sprang to life and significance only in the last paragraphs, where Wilkins briefly reported that his x-ray diffraction studies of intact sperm heads and bacteriophage—both, of course, containing a high proportion of DNA—gave patterns that suggested that DNA in living creatures has a helical structure similar to the model just proposed. The note by Franklin and Gosling came next. It was a revision and extension of their draft from the middle of March, in the light of the model. It presented the crucial diffraction photo structure B and analyze that and the other experimental evidence to show—with curt authority—that Franklin's data were compatible with Watson and Crick's structure.
"We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest."
"The biological significance of a two-chain nucleic acid unit has been noted (see preceding communication). The evidence that the helical structure discussed above does, in fact, exist in intact biological systems is briefly as follows: ..."
"Thus, while we do not attempt to offer a complete interpretation of the fibre-diagram of structure B, we may state the following conclusions. The structure is probably helical. The phosphate groups lie on the outside of the structural unit, on a helix of diameter about 20 Å. The structural unit probably consists of two co-axial molecules which are not equally spaced along the fiber axis, their mutual displacement being such as to account for the variation of observed intensities of the innermost maxima on the layer lines; if one molecule is displaced from the other by about three-eights of the fibre-axis period, this would account for the absence of the fourth layer line maxima and the weakness of the sixth. Thus, our general ideas are not inconsistent with the model proposed by Watson and crick in the preceding communication."
Lately there's been a flurry of activity in the American press about the value (or lack of value) of science. There have also been attempts by various organizations to enhance science education.1 Most defenders of science and science education will eventually end up trying to explain how science directly benefits the economy, usually in the form of return on investment. In other words, we need to do science because eventually the result will be used by somebody to make a profit.
I think this is a dangerous strategy. There are several ways of responding to the "what's in it for me" question without bringing up indirect economic benefit. These strategies are common when defending public support for the arts, for example. They're also used when defending research in the humanities.
Phill Plait of Bad Astronomy hits the nail on the head as far as I'm concerned [Wall Street Journal Editorial Board Member Gets Schooled on Science Funding]. His defense of science should be the primary talking point whenever anyone questions the value of learning about the natural world. Here's what Phil Plait says in response to Zack Kopplin's "return on investment" defense of science when Stephen Moore asks why the government is funding research on sex in snails.
How’s that for return on investment?
And that’s just a pedestrian, look-at-what’s-directly-in-front-of-you kind of thinking. We research the Universe around us because we are curious, inquisitive, intelligent animals. We don’t know what snail mating habits might teach us. That’s why we study it. Maybe it’ll lead into insight on how animals behave, or a new chemical secreted during the process, or to insight on the environment where snails live. Maybe none of that.
But that’s not the damn point. We study science because we want to learn about the real world. If we wanted to stick our heads in the sand, as people like Moore would have us do, he wouldn’t even have the venue he has to say ridiculous things like he just did.
Science is about exploration and discovery, and making sure we don’t fool ourselves. It’s among the noblest of all human endeavors, and something we should be both pursuing to our fullest abilities as well as defending from those who would drag it down.
Right on, Phil! Science leads to knowledge and knowledge is always better than ignorance. That's reason enough to fund science research and reason enough to support science education.
As sure as night follows day, there are going to be comments from people who advocate the "return on investment" strategy for defending science research. The argument frequently boils down to the fact that most politicians don't care about knowledge. All they want to see is how science can help business or improve the health and physical well-being of our citizens. Because these politicians are ignorant of the real value of knowledge, we must cow-tow to their ignorance and defend science on their turf.
That's what's happening in Canada with our Conservative government. In my field (biochemistry & molecular biology), many of my colleagues think we have to justify our research by showing how it will improve health. The current buzzword is "translational research." If you don't engage in the kind of research that Conservatives want, then you won't get funded.
Unfortunately, that may be true in today's climate. That doesn't mean we have to fool ourselves into thinking that that "translational research" be our primary goal. We recognize that the ignorance of our Conservative government is a problem, not a virtue. It's a problem that has to be fixed ... in the long term. Our goal should be to educate the next generation of politicians so we don't have to be embarrassed by them in the future. Let's at least have some people like Phil Plait who will speak out for basic curiosity-motivated research. We'll never succeed in convincing politicians and the general public of the value of knowledge if we don't even try.
Let's make sure we start with our students. Let's at least ensure that when we have them in our clutches as undergraduates we make sure that they understand science and the importance of knowledge. If we don't do that then we have nobody to blame but ourselves when future societies demand that science generate a return on investment.
Looking at my own university, it's obvious that we are not doing a very good job in our courses. I fear for the future of science.
1. In the USA "science" often gets lumped in with "technology," "engineering," and "mathematics"(=STEM) as though they had the same goals.
Imagine that you are speaking at a conference. You spent a long time preparing your talk and you have wonderful slides to illustrate your most important points. Imagine that half your audience doesn't seem to be paying attention. Their heads are down and they seem to be messaging on their smart phones or tablets. How do you feel about that?
Now imagine that there's a second screen behind you. One of them shows your wonderful slides but the other shows a continuous stream of tweets about your talk. That's the situation that PZ Myers encountered at a recent meeting [Good ideas and bad ideas]. PZ thinks this is a good idea, he says ...
One particularly interesting technological development was that there were two screens at the front of the room: one big one for the presenter to use, and a smaller one on which a twitter wall was displayed — all the silent conversations using the “#skeptech” hashtag were continuously displayed, which meant there was a constant flow of commentary from the audience sharing the stage with the speaker. It was rather cool — I’d like to see more of it at more conferences. It certainly made that hashtag explode with content.
I think that's a very, very, bad idea. I'm not sure that I would agree to be a speaker if I knew that the audience was going to pay more attention to their own tweets than to anything I was saying.
I wonder if PZ will incorporate this technology into his course lectures?
Scientific societies are made up of groups of scientists who band together for various legitimate purposes such as organizing meetings, publishing journals, promoting their speciality, and lobbying for funds. The credibility of a society depends on its area of expertise. They lose credibility when they take positions on issues outside of their discipline.
That's why many of us have been opposed to the accommodationist positions of the American Association for the Advancement of Science (AAAS) and other societies. These societies have no special expertise in epistemology/philosophy or religion yet they openly proclaim that science and religion are compatible. They should be neutral on that question. A (slight) majority of Sandwalk readers agree, according to a poll I took a few years ago [What Should Scientific Organizations Say about Religion?].
I wasn't alone in adopting this position. Jerry Coyne and PZ Myers also think that scientific societies should keep their nose out of areas that are outside of their mandate. We are united when it comes to opposing accommodationism.
Many of you will remember the "arsenic affair" from a couple of years ago. Here's what I wrote in February 2012 once we knew that the main result of the paper had been disproven by Rosie Redfield. We now know that there was no arsenic in the DNA (Erb et al. 2012, Reeves et al., 2012).
The "arsenic affair" began with a NASA press conference on Dec. 2, 2010 announcing that a new species of bacteria had been discovered. The species was named GFAJ-1 (Get Felisa a Job), by the lead author Felisa Wolfe-Simon. GFAJ-1 was grown in a medium that lacked phosphate and contained high concentrations of arsenic. The paper, published that day on the Science website, claimed that arsenic was replacing phosphorus in many of the cell's molecules, including nucleic acids.
Like many other scientists, I was very skeptical from day one. The results reported in the press conference just couldn't possibly be true unless everything we knew about chemistry and DNA was very wrong.
How did this paper ever get published in Science? I was suspicious that the normal peer review process had been skipped in order to get a major discovery into press as soon as possible.
The manuscript Wolfe-Simon et al. demonstrates for the first time that a microorganism is able to use arsenic in place of phosphorus to sustain growth and life. This was done by using a rather simple initial selection on synthetic growth medium followed by a more in-depth analysis of the isolated organism with regard to the path of arsenic from uptake to incorporation into various cellular fractions using ICP-MS, 73As labeling and X-ray absorption near edge spectroscopy (XANES).
The results are exceptional as they show that arsenic, yet believed to be highly toxic for most organisms, in GFAJ-1, a member of the Halomouadaccae, can substitute for the lack of phosphate, a major building block for various macromolecules present in all cells, namely nucleic acids, lipids and proteins.
The methods applied are straightforward. The most surprising and acknowledgeable aspect of the work is its simple approach.
I have only a few minor points regarding the overall presentation.
Review 2
The manuscript by Wolfe-Simon et al. is well-written, concise, to the point and provides exciting novel results. The authors provide many lines of evidence to prove their point that the isolated novel bacterium (at least to some extent) can replace phosphate by arsenic in its biomolecules. It's a pleasure to get a well-conceived and carried-out study to review.
Review 3
Reviewing this paper was a rare pleasure. It is clearly-written and well-reasoned. The authors choose the right methods, designed the right experiments, obtain solid data supporting the conclusion that GSAJ-1 uses As in place of place of P. They use appropriate caution in interpreting results. I think the paper is just about publishable as is; my comments for revision are below. Great job! I look forward to seeing follow-up work in the future.
Looks like we can blame the reviewers, or perhaps the editor for choosing the wrong reviewers.
[Hat Tip: Michael Eisen (@mbeisen) (#arseniclife)]
Erb, T.J., Kiefer, P., Hattendorf, B., Günther, D., and Vorholt, J.A. (2012) GFAJ-1 is an arsenate-resistant, phosphate-dependent organism. Science, 337: 467-470. [doi: 10.1126/science.1218455 ]
Reaves, M.L., Sinha, S., Rabinowitz, J.D., Kruglyak, L., and Redfield, R.J. (2012) Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science, 337: 470-473. [doi: 10.1126/science.1219861]
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-1166. Published online 2 December 2010; published in Science magazine Jun 3, 2011 [doi: 10.1126/science.1197258]
I've said it before and I'll say it again, biology is messy. It's really hard to rigorously define simple terms because there are always exceptions. Just think of the problems we've had trying to define a gene [What Is a Gene?].
"Mutation"¹ is almost as difficult. First, we want to distinguish between a mutation and DNA damage. DNA damage occurs when various enzymes make a mistake and damage the nucleotides in a DNA molecule. Damage also occurs when outside forces such as X-rays or chemical mutagens attack DNA. Examples are thymidine dimers or cleavage of a base from a nucleotide. DNA can also be broken into two or more pieces.
This damage is never copied and passed on to the next generation. Either it is fixed in some way or it is lethal. When the damage is fixed it may end up being identical to the original DNA molecular or it may be altered in some way that is passed on. Thus, mutation is (semi-)permanent change that is heritable.
In the example shown here, the damage is deamination of cytosine, a very common spontaneous reaction. It is usually repaired fairly quickly but if the DNA is replicated before repair it will result in a switch from a G/C base pair to an A/T base pair at the same site. This change is inherited in all subsequent generations ... it is a mutation.
The genetic material is DNA in most cases but RNA genomes (viruses) can also be mutated. There are many different kinds of "genomes" that have to be covered in our definition. This include virus genomes, mitochondrial genomes, chloroplast genomes, plasmids, and mobile genetic elements (mostly transposons).
Any alteration in the sequence of a genome counts as a mutation, not just those that occur in a gene (whatever that is!). This is important because some of the traditional definitions of mutation are restricted to genes.
Here's a good definition from the Wikipedia site ...
In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. Mutations result from unrepaired damage to DNA or to RNA genomes (typically caused by radiation or chemical mutagens), from errors in the process of replication, or from the insertion or deletion of segments of DNA by mobile genetic elements.[1][2][3] Mutations may or may not produce discernable changes in the observable characteristics (phenotype) of an organism.
The Understanding Evolution at UC Berkeley defines mutation as ...
A mutation is a change in DNA, the hereditary material of life. An organism's DNA affects how it looks, how it behaves, and its physiology. So a change in an organism's DNA can cause changes in all aspects of its life.
This isn't good because it doesn't cover RNA genomes and it doesn't distinguish between DNA damage and fixed, heritable, change.
-definition -mutation types -mutation rates -phylogeny -controversies The Genetic Science Learning Center at the University of Utah offer this definition.
A mutation is a permanent change in the DNA sequence of a gene. Mutations in a gene's DNA sequence can alter the amino acid sequence of the protein encoded by the gene.
That's no good because it restricts mutations to protein encoding genes.
A quick Google search will reveal many other definitions but none as as good as the Wikipedia entry.
As usual, the standard dictionary definitions are not helpful. They are usually quite poor at defining biological terms. Merriam-Webster defines mutation as ...
a relatively permanent change in hereditary material involving either a physical change in chromosome relations or a biochemical change in the codons that make up genes
This is actually better than some of the definitions from scientists. It's main deficiency is that it restricts mutations to genes.
1. The word comes from the Latin mutare, to change.
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It seems obvious to most of us that engineers and physicians are not scientists. PZ Myers mentions this on his blog when he discusses the debate as reviewed by William Saletan: Saletan is at it again. Here's what PZ says ...
This would be unremarkable except that Jason Rosenhouse disagrees [Saletan vs. Myers on Nye vs. Ham]. Here's what Jason says ...
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