Bless their hearts. The Creationists over at Answers in Genesis are working their perfectly designed fingers to the bone. Blowing the Discovery Institute out of the water by not only publishing a for-realsies science journal (well, at least once), but also performing 'semi-technical' research!
Darwin at the Drugstore? Testing the Biological Fitness of Antibiotic Resistant Bacteria
While its just adorable to see them working so hard, their crippled understanding of basic science leaves this semi-technical article completely worthless.
Problem #1-- Comparing Chihuahuas to Great Danes
If *I* were designing a similar experiment, I would have used two types of bacteria.
- Bacteria A- susceptible to ampicillin
- Bacteria B- genetically identical to Bacteria A in every way, except resistant to ampicillin
Thus if there is a fitness difference between the two bacteria, I could be 100% sure it was because of the ampicillin resistance, not anything in the genetic background muddling things up.
This is not crazy magic work.
I am not making unreasonable demands.
That is exactly what I do in my experiments. I take a 'white mouse' version of HIV-1, called NL4-3. I chop out a bit of it, and paste in regions from patient samples. All of my viruses are 100% identical, except for the bit I pasted in, so if there are fitness differences between my viruses, I know it has to be genetic differences in the bit I pasted in causing the effect.
Yeah. They didnt do that.
They took two kinds of bacteria with the same species name and compared them. The 'wild type' strain they got from a friggen pond. While that is the cutest thing ever, you cant do that. They have no idea what its genome looks like. They dont know if phenotypic differences between the bacteria are because of antibiotic resistance or because of other genetic differences.
Problem #2-- 'Fitness' doesnt mean what they think it means.
What does it mean to be a 'less fit' variant? When Im competing various viruses against one another, I define 'fitness' as who infects the most cells in a certain environment. Virus A might be a wussy loser on dendritic cells, but a deadly monster on macrophages. Virus B might tear up every cell you feed it, but is easily neutralized by antibodies. 'Fitness' changes depending on the environment, and how you define it, and how you measure it.
This paper defines 'fitness' as 'growth rate and colony "robustness" in minimal media'. Considering Problem #1, we have no idea whether the 'smaller colonies' or a delayed log phase in the antibiotic resistant bacteria are because of the antibiotic resistance... or something else.
Additionally, their 'growth curve' (Figure 2) is useless. A growth curve with no error bars. A growth curve that shows two types of bacteria reaching an identical stationary phase at the same time. Which leads me to believe that if they had performed this experiment more than once, the error bars of these two bacteria would overlap, ie, there is no significant difference between the growth kinetics of these two bacteria. Just like there is not a growth difference between the bacteria in rich media.
But lets grant their premise. The antibiotic resistant Serratia marcescens is 'less fit' than 'wild type'.
Then why does antibiotic resistant Serratia marcescens makes up 92% of the Serratia marcescens infections in hospitals (according to their paper)?
Because while antibiotic resistant Serratia marcescens might be 'less fit' in 'minimal media', they use ANTIBIOTICS in hospitals. And in the presence of ANTIBIOTICS the ANTIBIOTIC RESISTANT bacteria has a clear reproductive advantage: IT DOESNT DIE.
You have to use an appropriate definition for 'fitness'.
Problem #3-- 'Comparison' does not mean the same thing as 'competition'.
I compare viruses every day. I infect a set number of cells with a set number of viruses, and I count how many cells get infected. Lets say in these mono-infections, Virus A infects 90% of the cells, and Virus B infects 90% of the cells. Are these two viruses equally fit?
Hmm. The key to this game is 'competition'. Throw two kids in a room full of Cheetos, and youre going to have two very obese, very orange children. BUT! Throw two kids in a room with a snack sized bag of Cheetos... one of those kids is going to eat, and one of those kids is going to get a black eye.
To compete viruses, I put the same amount of Virus A and Virus B onto a set number of cells, and I scream 'FIGHT! FIGHT FIGHT! FIGHT!' Virus A and Virus B have equal 'odds' of infecting cells at that point, so if theyre about the same, they will infect the same number of cells (50/50). However, if Virus A is better in that particular environment, it might infect 90% of the cells, while B dawdles around and can only claim 10%. Its a head-to-head battle for limited resources.
Despite the fact the word 'compete' is uses multiple times in this article, nothing is 'competed' in this article. Two different bacteria are 'compared'. There is a difference.
Look, I know relatively little about bacteria. They arent the 'micro' in microbiology Im most interested in. But I can do a basic PubMed search to find a paper that analyzed the fitness cost of antibacterial resistance in Serratia marcescens the hard way (ie, the right way):
A Fitness Cost Associated With the Antibiotic Resistance Enzyme SME-1 Î²-Lactamase
Its a little more than 'semi-technical', but they do things right. From their discussion:
Antibiotic resistance that occurs via mutation of an antibiotic target often results in a fitness cost to the bacteria under permissive conditions. This suggests that the removal of antibiotic pressure will reduce the prevalence of resistant bacteria. However, the effectiveness of this strategy is dependent upon a fitness cost that can be overcome or reduced in several ways. First, antibiotic resistance genes are often genetically linked in the form of multi-resistant mobile DNA elements and selection of one resistant determinate can result in the maintenance of other resistance genes by linkage. Second, fitness costs are typically negated by the appearance of compensatory mutations that alleviate the fitness cost while preserving the resistance phenotype. Without a significant fitness cost, there is no selective pressure to drive a loss of the resistance determinant. Finally, multiple routes of resistance can exist and be highly variable with regard to the fitness costs they engender. Therefore, a spectrum of resistant clones can exist; some with no fitness costs or even enhanced fitness under permissive conditions. (references removed for ease of reading-- ERV)
*sigh* Its really, really cute that Creationists are trying to do big-kid research. But 'Darwin at the Drugstore?' is just a friggen mess.
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What a pathetic excuse for a scientific paper. I know I have read abstracts by Intel Science Talent Search semifinalists and finalists who were seniors at Stuyvesant, Bronx Science, and several Long Island public high schools that were real scientific abstracts (though one of my favorite ones was pertaining to behavioral ecology by a New York, NY private school senior).
I wonder how much science they had to copy from Carl Zimmers magnificient, recently published book.
P. S. Dave Wisker has a rather astute comment over at PT which I hope he posts here too.
Impressive. They didn't even compare read and white sensitive strains, to remove the effect of the colour morphology.
You were kind enough to the authors to overlook this:
i.e. "we didn't find any differences, so we played around with the conditions until we did".
I wish I got papers like that to review. It would be much more fun.
Abbie, how cute, you treated it like it was real science!
We all know it is really part of an odd publicity scheme...See, we've published in "peer reviewed" journals! Granted, we had to create them ourselves because nobody is going to allow the geology article I checked out - the one about how evidence from granitic rock supports the 6,000 year old Earth - to be published. It doesn't really matter what the articles say so long as they can tell a public that doesn't really understand science that "we" published in scientific journals - just like real scientists.
I thank you for the link as I was thinking about a good way to introduce students in my Ecology and Evolution course to pseudoscience (also a good time to expose them to critical reading) and I'm sure I can find a great article in this "journal".
I wonder if they allow responses/comments on articles, you know, like real journals?
Way to go Abbie! Not only did you destroy the Creo's toy experiment, you also destroyed DaveScot's world-view, and probably made him cry as you totally failed to swear and curse at a Creo. Not even ONCE??!!
Dear Dr. J,
I wouldnt even try to dignify this publication as one in a peer-reviewed scientific journal since the journal doesnt provide a list of those on its editorial board (Hmm, let me guess. Dr. Michael Egnor of SUNY Stony Brook? Dr. Kurt Wise, who, as a Ph. D. candidate in paleontology at Harvard University, was a student of Dr. Stephen Jay Gould? Dr. Ken Ham, perhaps?).
Nor would I agree with Abbies assessment that this would be an acceptable middle school science project. Certainly not in any of the public, private or parochial middle schools I know of in New York City and on Long Island. Any qualified science teacher would recognize this instantly as pseudoscientific nonsense and direct his/her students to pursue a research topic that was truly scientific.
Even though they used a chapter heading from my book for their post title, I take no responsibility for the contents of the post (or lack thereof)!
Thanks for writing this (and for the link to the good Serratia paper--I'll check it out).
Like Steve Gould, Genie Scott, and Niles Eldredge, among others, you've become yet another "victim" of a typical creo pastime, "quote mining". Thankfully what you write is always quite credible (A lesson which I wish your "colleague" Suzan Mazur would learn soon, if you've noticed the recent discussion about her over at PT.).
Ack. My biggest concern about this is how to keep this on-line 'journal' out of the library's science sections. Presumably the science librarians are savvy enough not to list it among the other electronic journals they have available - but how do we let our students know it's not considered valid? Do we now have to start a list? "For your paper, include at least 3 peer-reviewed journal articles, so long as they are not from the following journals, since we don't consider their peer-review valid science:"
? ideas ?
Doesn't it remind you of little kids playing school?
Alas you may have to tell your students TO IGNORE "journals" like these by having a disclaimer of the kind you've suggested. Wish I could think of a simpler, more elegant solution, but with the creos "playing" like - as Bill the Cat suggested - "little kids playing school" - then you'll have to be vigilant.
Hope this helps.
It might be more fruitful to take the time and go over a pseudoscientific "journal article", like the one Abbie demolished here. Use it as an opportunity to teach good science while simultaneously showing what bad science looks like. Then, when you say, "The following so-called journals were created to make a home for garbage like this," your statement will have some genuine weight.
Abbie, you forgot horizontal gene transfer! Shame on you.
And why did they choose to play with ampicillin resistant Serratia? No physician worth her/his salt would choose to treat a suspected gram-negative infection with ampicillin alone anymore.
Unfortunately your advice is exactly what the DI's intellectually-challenged crowd of acolytes and sympathizers are hoping for with their "academic freedom" bills. Far more productive usage of a teacher's time would be explaining why mainstream science is valid science, not to go on at some length in demolishing inane pseudoscience of the kind published in AiG's "journal".
I appreciate the point that a teacher's time is finite and sharply bounded, but I don't think it's a foregone conclusion that debunking a few items of pseudoscience is a waste of that time, nor do I think that an argument from authority is a good guard against pseudoscience (speaking on both philosophical and practical grounds). I don't even think "explaining good science" and "debunking bad science" exclude each other. Look at this very post: we learn about splicing snippets of DNA into HIV-1, and we explore how fitness depends on ecology.
Take half a lecture out of a whole semester and use it to dissect a shoddy piece of research. If you don't want to go too far down the sliding scale, perhaps pick a bad study with a legitimate aim, or a paper which was good in its day but has flaws only recognized later. Then we learn not just what the good science is, but what flawed science looks like.
Crap of the AIG variety might be too far beyond the pale to bother with, but if you spend half an hour on something only moderately bad, then you can still say, "The following so-called journals were made to give a home to garbage that's far, far worse."
If it's no more than half a lecture than I am in full agreement with you. However, I will note that British filmmaker Matthew Chapman has advocated in his book, "40 Days and 40 Nights" (His memoir of the 2005 Kitzmiller vs. Dover trial) devoting ample time in the classroom in "dissecting" Intelligent Design creationism alongside genuine science (An argument which, I believe, would have mystified his notable ancestor, Charles Darwin.).
I still stand by what I wrote in the concluding paragraph to my Amazon.com review of Chapman's book:
"Chapman concludes '40 Days and 40 Nights' on a most idiosyncratic, personal note, and one that he has alluded to ever since the very first page of his memoir. He contends that we should allow creationism into the science classroom, so that it can be 'dissected', in much the same fashion as it was during the Kitzmiller vs. Dover Area School District trial, by allowing teachers to 'explore the limitations of faith through the revelatory methods of science', and resulting in 'verdicts' identical to Republican Federal Judge Jones' conclusion that Intelligent Design wasn't scientific. Emotionally, it is a sentiment that I found myself quite unexpectedly, at first, to be in complete agreement. However, on second thought, I concur with Ken Miller's observation that introducing Intelligent Design into science classrooms would be a 'science stopper'. It would conflate most students' understanding of what exactly is the difference between religious faith and science, though I suppose that some truly gifted students, like those attending prominent American high schools such as Alexandria, Virginia's Thomas Jefferson High School for Science and Technology, and New York City's Bronx High School of Science and Stuyvesant High School, might readily understand and appreciate these distinctions. And yet I am inclined to agree more with the harsh view articulated by distinguished British paleontologist Richard Fortey in his essay published in the January 30, 2007 issue of the British newspaper Telegraph, contending that it is an absolute waste of time arguing with Intelligent Design advocates, and that they ought to be dismissed as 'IDiots'; by extension, so would be the teaching of Intelligent Design alongside evolution in a science classroom. I would rather see talented students from Thomas Jefferson, Bronx Science and Stuyvesant engage themselves fruitfully in genuine scientific research of the highest caliber, than in trying to understand the metaphysical, religious nonsense known as Intelligent Design and other flavors of creationism. I think, in hindsight, so would Charles Darwin."
Moreover, I think a truly gifted science teacher need not make an "argument from authority" in explaining why AiG's version of "scientific creationism" is pseudoscientific nonsense; all he/she would have to do is to explain the logic of scientific discovery, by noting how the "material naturalism" of the scientific method has served both science and Western Civilization well since its inception in the 16th and 17th centuries.
PS to my last comment:
By "material naturalism", I actually meant to say, "methodological naturalism", which, I believe, is the term used by Bill Dembski, Phil Johnson and their fellow Discovery Institute mendacious intellectual pornographers.
The part of how you splice bits from one virus to another both baffles and intrigues me. Exactly how does that work? I can't quite wrap my mind around how that can be done to a virus as opposed to a cell. Also, how do you keep endless supplies of virii? Do you have an evil breeding program in your evil laboratory in your evil volcano lair? ;-) Just wondering. :)
It looks like we agree more than we disagree. I should have been more explicit in my first comment; for that, I apologize. I suspect that "the logic of scientific discovery" cannot be taught without reference to the mistaken ideas we had at earlier stages of our intellectual development. Giving a little bit of time to Ptolemaic astronomy and the phlogiston model of heat is common practice where I come from — the better to understand how those ideas were superseded.
The ARJ also has a nice paper on peer review for creationists. It can be summarised thusly:
* the word "peer" means "equal"
* the peers of mendacious creationists are other mendacious creationists
* therefore it is correct to call it "peer review" when creationist mendacity in the form of pseudo-scientific mimicry is praised by other creationists as a significant contribution to mendacity and general untruth
* oh, and here's a load of quote-mined citations of nibbles of the Holly Bibble to justify our mendacity, hypocrisy and general unworthiness to walk on this world (see, they devalue Christianity by quote-mining just as they try to devalue science by quote-mining!)
* and, probably, Christians invented peer review (if it's A Good Thing)
WhhhheeeeeeEEEEEE!! My head spins round with the cretinosity overload!!
Thanks for all the suggestions on how to deal with this in class, interesting discussion.
Sam C - I read the peer review article as well, but I had quite a different take on it. I thought they talked big about how scientifically rigorous they should be, and how it was their duty not to present things as science if they are not, which sounds great but clearly isn't being applied in the reality of the peer review process. I actually blogged about it, I was so intrigued: http://jerseydevil77.livejournal.com/24636.html
'Tis an old trick of science cranks. Feynman on cargo cult science:
This journal is explicitly following the archetype; predetermine your result, making faux experiments, cherrypick those that points to your chosen explanation, and publish by 'peer review'. It is a game AFAIU as old as science has shown itself to be successful.
I'll admit that I'm curious too. But why wouldn't they work with the virus as expressed in the cell then?
Btw, that reminds me of this article claiming that part of our virus defense is to mutate virus in the cells:
To add to the list of failed creationist ideas - not only do we have clear evidence of inherited ervs since millions of years, we may have clear evidence of inheritance of the then immune response to them.
Uups, I meant press release. Haven't read the article.
I'm reminded of Dresden Codak, when Kimiko was a toddler: The received a cookie and declared "I will do science to it."
Maybe "We will do SCIENCE to it!" should be AiG's new catch phrase...
megan @ #8,
Here's a nearly foolproof way to insure that students only use bona fide peer-reviewed scientific research journals. Require that the journals are indexed at the National Library of Medicine. While this does let Rivista di Biologia slip through the cracks, it completely stifles the creationist journals.
Of course, students should also be taught to be suspicious when a journal has a header like this:
Answers Research Journal (ARJ) is a professional, peer-reviewed technical journal for the publication of interdisciplinary scientific and other relevant research from the perspective of the recent Creation and the global Flood within a biblical framework.
Not science, move along.
Another clue is citation of Bible verses in the text.
And for this paper, another tipoff is:
by Dr. Alan L. Gillen and Sarah Anderson, Liberty University
For anything dealing even remotely with evolution, that can be tossed right into the trash bin.
I really should drop some webcomics and make room for Dresden Codak. It seems to be one of the best newcomers from what I hear of it.
Who is this John guy? And why is he responding to everyone's comments? Will he respond to mine with a long "Dear Chris" letter?! I sure hope so!
The creation museum is like two hours from me, and yet I've not been there. Maybe I'll venture down in August, but I just can't find any reasonable excuse to give them my money. I think the comedic value would be outweighed by the terrible pain I'd feel from the high level of stupidity gathered in that place.
I also like how their only 'data' in the paper is absorbance - using pigmented vs. non-pigmented bacteria! Prodigiosin (the red pigment), as it turns out, doesn't absorb too strongly at 620 nm. But you kind of have to address that. At the very, absolutely minimally least, cite something that says "Well, the prodigiosin absorbance isn't a big deal." What you should do is prove that equal absorbances = equal # of bacteria by serial dilution plating. Even if you're not dealing with red vs white bacteria.
If ARJ were a legitimate scientific journal, then they would have to also publish reasonable rebuttals to creationist articles. In fact, with a little cleaning up, this blog post could be a good letter to include in a future issue. Alas, I'm pretty sure that ARJ is not legitimate.
Indeed, Abbie's reply would never get past their criteria for publication.
Yay! No response letter yet! Whoo-hoo! :-)
Naaah, only joking.
Seriously though Chris, how could you not have noticed John? He's been posting here to a while now.
Hi manigen and Chris,
I do have a life outside of posting at Abbie Smith's terrific ERV blog, such as tending to my Amazon.com reviews and comments and posting over at PT. Seriously, there's other matters to keep me preoccupied. I don't have as much as time as I would like to devote to posting here.
However, more importantly, I hope whatever I have been posting of a serious note has been something you've read carefully and given ample thought. Certainly Blake Stacey has.
This is the kind of thing we need more of; not just data showing that their facts are either wrong, out-of-date or misquoted, but detailed examination of the few "experiments" that they do do in order to show that they don't know what they're doing.
Any one have any idea where there's been more analyses of creationist "experiments"?
A collection of those would make a useful book and teaching tool in real science classes as to why creationism isn't science.
Off topic rant below:
I guess Dembski's still smarting from having one of his supporters being a member of the "pleasurians"...in his latest screed (Olivia Judson: "Let's not call what we're doing 'Darwinism'.") he posts a picture from a project this Judson woman is doing with the caption CAPTION: OLIVIA JUDSON BUSY AT HER RESEARCH.
At least he provides the link so you can go and see what's really going on. That's not her research, that's from a documentary she's made where she tries to present the biology of sex in a manner that's entertaining. It's a stupid and juvenile way to do it, but unlike Dembski, she at least knows what she's doing and the article linked to shows that it's entertainment.
Hello John. Of course I've read a fair few of your posts, and you've made some interesting points. If I wasn't such a perpetual lurker I might have tried to respond.
And, of course, I stand in awe of Blake's analytical abilities.
More of the same "frat-boy antics" which we've come to expect from my "pal" Bill Dembski, which I have posted here:
In fact, there's been some excellent commentary on Olivia Judson's photo from me and a fellow Amazon.com customer posting there at that discussion thread.
Yes, Blake is a very good poster, but there are others who have been doing a rather excellent job of it over at PT (Stanton and raven, among others) and fellow NCSE members Tim Beazley and David E. Levin, and also Mary Endress, at Amazon.com. You should read their remarks as well as a few of mine over at Amazon.com and PT.
Hmmm...I guess I must have missed John's comments. I usually only read Abbie's posts. I don't comment enough on her blog, but I'm trying to change that! :-)
Also, what's PT? I thought maybe it was PZ...
PT is shorthand for "Panda's Thumb" (www.pandasthumb.org), which features excellent blog entries from the likes of former NCSE staffers Wesley Elsberry, and Nick Matzke (though regrettably less so since Nick started graduate school last year) and PZ Myers, among others. Abbie has been posting there occasionally since last summer. IMHO, Panda's Thumb is still the best blog devoted to evolution and, especially, the so-called "evolution vs. creation" debate.
Chris (Fabulously in the City) said:
PT stands for Panda's Thumb. A rather interesting, and informative science blog. They also have a forum associated with it, and a lot of the inside jokes, and some of the lexicon that Abbie uses comes from there.
Thanks, John. I was hoping that this would be stored somewhere to showcase what kind of person he was...though I don't have the URLs to all those incidents.
At least now I know where to look.
Try googling Richard Dawkins' website, www.richardawkins.net, for David Bolinsky's open letter (which mentions Dembski's theft of the XVIVO video), Abbie Smith's post on her former blog about Bill's "friendly" act towards me back in December, and also check both PT and Uncommon Descent (www.uncommondescent.com). I've also posted some links in several of the science discussion threads - especially those I created like the one about Bill Dembski whining and moaning about "rich Darwinists" like Ayala, Dawkins and Miller.
Regards (until tomorrow),
PS. Am referring of course to the Amazon.com discussion threads on science.
Oh, thanks all for the explanation :-). I've been there (PT) previously, I just don't read it as religiously as I do erv/Pharyngula. :-)
I know this is off-topic, but I'd like to note the passing of a college classmate, computer scientist Randy Pausch, who was well-loved by his students and colleagues, and highly respected as both an educator and researcher in computer science:
I honestly don't think I know of any Intelligent Design advocate or other creationist teaching at a college or university who was as well loved or as respected as Randy was.
I read that whole thing. It was mostly empty stuff. Their "experiment" fulfilled predictions of the modern synthesis: that increases in specificity of organisms in response to some environmental stimulus will be a benefit in presence of that evolutionary pressure. And that organisms that expend more energy in a way that doesn't lead to increases in reproductive success, will not be favored. From there adaptive radiation of more conservative organisms will lead to higher representation of organisms that conserve energy.
These creationists basically stumbled upon the reason why cave-fish only have vestiges of eyes.
BTW why is it that creationist make such grandiose claims about the glory of god's world but continue to have this mindset that everything was perfect in the Garden of Eden and that humans can only expect things to get worse and worse over time?
What could possibly be more corrosive to society that we can better our own world? That's what the dark ages were all about.
Re John Kwok
A minor correction. Thomas Jefferson High School is located in Fairfax Co., Virginia, not in the City of Alexandria.
Thanks for the correction. I have read references to Thomas Jefferson High School as being located either in Fairfax Co., Virginia, or in Alexandria, Virginia (which is part of Fairfax County).
Didn't they just end up demonstrating (and wasting a lot of time and money) what was known above?
||Studies of the evolution of resistance often show that you don't get something for nothing. Specifically, it "costs" a pest or pathogen to be resistant to a pesticide or drug. If you place resistant and non-resistant organisms in head-to-head competition in the absence of the pesticide or drug, the non-resistant organisms generally win.||
I love it when creationists score on our goal.