Tag: New York Times

Pleasantly surprised by the National Microbiome Initiative

So I got this email a few weeks ago inviting me to the White House.

Not every day that I get invited to the White House.  And I thought I was probably on their shit list after removing my name from the “Unified Microbiome Initiative” paper due to it being non open access.  So I asked a colleague if she could teach in my large introductory biology class for me on May 13 and she said yes.  So I RSVP to the meeting and told my mom I would be coming to the DC area (where I grew up).  And I told everyone, proudly “I am going to the White House”.

I realized I had a tight schedule for flying in and out since I had to be back in Davis Saturday AM.  So I wrote to the White House to ask about the schedule for the event.  You see, I had no information as to what this event was going to be about.

And, they did tell me this would work although they would not tell me what the meeting was about.

I then bought my tickets and got excited to be going to the White House.  However, fate would not be so kind to me.  My daughter got sick last week (bronchitis, and multiple spin off issues) and so I started to wonder if I really should go away.  So I tried to find out what was happening at this event.  I wrote a few friends who I knew were going and one of them told me there would be a series of talks and another told me they did not know.  So – without much other information to go on, and with a strong desire to take care of my daughter as much as possible, I cancelled my trip.

Then yesterday I got an email from a NY Times reporter

And so we connected and talked for a bit.  I found out from the phone call that the White House was announcing their Microbiome Initiative (which I knew was in the works but for which I basically knew no details).  The reporter Gardiner Harris asked me how I felt about “Big Science” types of projects and, well, I did not say nice things about them.  And I stand by those critiques of Big Science.  I talked about how I disliked the Human Microbiome Project in many ways because it fed too much money to a few groups and was prone to the same problems of other Big Science projects.  And that they were generally a waste of money.  We also discussed how I thought science worked better when administrators got out of the way and let peer review have more of a role in determining what was important.  And I said that if the new White House initiative was another top down science effort, then this would likely be a bad thing.  Or something like that.  But I did also say that I had no idea what the White House was going to announce about and I hoped it was more supportive of small science.

So the article came out and I was featured in it

Definitely something I stand by.  I think top-down approaches to science do not work well.

I woke up early this AM and started posting about the evils of Big Science.  And then I finally found an announcement with actual details on the National Microbiome Initiative being announced today.  And I was pleasantly surprised.  This was not about a big, top down approach to science.  It was more about a collection of projects under one big umbrella theme of microbiome studies.

Yes there were some top down aspects to it.  But only a component. So once I saw this, I realized my quote in the NY Times was not ideal.  Yes Big Science is bad.  But this National Microbiome Initiative is not really the standard bearer of Big Science.  It is not really even Big Science.  It is more   of a “Organizing Distributed Science”.

And I found one article out there about the project that captured this essence of it:  The White House Launches the National Microbiome Initiative  by Ed Yong in the Atlantic. He nails it with this section

The National Microbiome Initiative is not the Human Genome Project—a single project with a definitive goal. It consists of many organizations operating independently; to paraphrase Whitman, it contains multitudes.

So my quote in the NY Times was technically correct – Big Science is bad.  But it also not quite right in the context it is presented – since the NMI is actually not really (or at least not completely) Big Science.  I do wish the context of the quote had been presented a bit more  (well, more specifically that I did say I did not know the full details of what they were actually proposing).  Lesson learned.  Be really careful about commenting about things “generally” without knowing the details.  I definitely regret doing that here.  I did in fact say what is reported so can’t complain about being misquoted.  But I should have been more careful regarding the caveats and context.

I note – it is unclear to me how much of these smaller distributed projects would have happened without the NMI.  My guess is most of them would have happened and that the NMI is a bit of a public relations effort.  Ed Yong also captured this issue in his piece:

A cynic might be forgiven for seeing this as an exercise in branding, encapsulating what microbiome scientists were already doing under a catchy umbrella.

And I also worry as always that “Microbiomania” (hype about the microbiome) will get worse with this announcement of the NMI.  And it probably will.

But in the end I am very happy that this is not a run of the mill top down Big Science project (like the Human Genome Project or the Human Microbiome Project or the Human Brain Project).  It is much more nuanced than that.  Much more distributive.  Much more likely to support small science and creative science and such.  And that is a good thing.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

The flawed and offensive logic of "Academic Science Isn’t Sexist" in the @nytimes

OK.  It is Halloween night and I am tired and need to get my kids to sleep.  But someone on Twitter just pointed me to an opinion piece just out in the New York Times: Academic Science Isn’t Sexist – NYTimes.com and after reading it I felt I had to write a quick post.

The opinion piece is by Wendy M. Williams and Stephen J. Ceci and discusses work by them (and coauthors).  In particular they discuss findings in a massive report “Women in Academic Science: A Changing Landscape” by Stephen J. Ceci, Donna K. Ginther, Shulamit Kahn, and Wendy M. Williams in Psychological Science in the Public Interest.  I note – kudos to the authors for making this available freely and under what may be an open license and also apparently for making much of their data available behind their analyses.

The opinion piece and the associated article have a ton of things to discuss and ponder and analyze for anyone interested in the general issue of women in academic science.  I am not in any position at this time to comment on any of the specific claims made by the authors on this topic.  But certainly I have a ton of reading to do and am looking forward to it.

However, I do want to write about one thing – really just one single thing –  that really bothers me about their New York Times article.  I do not know if this was intentional on their part, but regardless I think there is a major flaw in their piece.

First, to set the stage — their article starts off with the following sentences:

Academic science has a gender problem: specifically, the almost daily reports about hostile workplaces, low pay, delayed promotion and even physical aggression against women.  Particularly in math-intensive fields like the physical sciences, computer science and engineering, women make up only 25 to 30 percent of junior faculty, and 7 to 15 percent of senior faculty, leading many to claim that the inhospitable work environment is to blame.

This then sets the stage for the authors to discuss their analyses which leads them to conclude that in recent times, there are not biases against women in hiring, publishing, tenure, and other areas.  Again, I am not in any position to examine or dispute their claims about these analyses – to either support them or refute them.

But the piece makes what to me appears to be a dangerous and unsupported connection.  They lump together what one could call “career progression” topics (such as pay, promotion, publishing, citation, etc) with workplace topics (hostility and physical aggression against women).  And yet, they only present or discuss data on the career progression issues.  Yet once they claim to find that career progression for women in math heavy fields seems to be going well recently, they imply that the other workplace issues must not be a problem.  This is seen in statements like “While no career is without setbacks and challenges” and “As we found, when the evidence of mistreatment goes beyond the anecdotal” and “leading many to claim that the inhospitable work environment is to blame.”

Whether one agrees with any or all of their analyses (which again, I am not addressing here) I see no justification for their inclusion of any mention of hostile workplaces and physical agression against women.  So – does this mean that a woman who does well in her career cannot experience physical aggression of any kind?  Also – I note – I am unclear I guess in some of their terminology usage – is their use of the term “physical aggression” here meant to discount reports of sexual violence?   This reminds me of the “Why I stayed” stories of domestic violence.  Just because a women’s career is doing OK does not mean that she did not experience workplace hostility or physical or sexual violence.  I hope – I truly hope – that the authors did not intend to imply this.  But whether they did or not, their logic appears to be both flawed and offensive.

UPDATE 1. November 1, 8:30 AM

Building a Storify about this.

UPDATE 2: Nov 3, 2014. Some other posts also criticizing the NY Times piece

UPDATE 3: Nov. 4, 2014.  More posts about the NY Times piece
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Overselling the microbiome award – many – for stories about placental vs. oral microbiomes

A few days ago on Twitter I was pointed to a news story about the human microbiome:

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I looked at the article and definitely agreed with Ed. So I responded

//platform.twitter.com/widgets.js And then a mini conversation happened

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And I pondered writing up an “overselling the microbiome award” but I got caught up in other things. And then today some people (including Jens Walter) pointed me to this New York Times article about the same topic: Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com. And I decided I had to write something up because too many news stories were not doing a great job with the science here.

So here goes. First, the Science news (UPDATE – NOTE this is the news part of Science magazine, not ScienceNewsOrg) story Ed Yong pointed to originally and the parts I have problems with.

  • Sentence 1: Researchers have discovered a small community of bacteria living in a most unlikely place: the placenta, the organ that nourishes a developing fetus through the umbilical cord.  No – not really.  They did not discover this.  They did a more detailed characterization of the community.
  • Sentence 2: The finding overturns the conventional wisdom that the placenta is sterile.  No – the study is another piece of evidence that argues against the “conventional wisdom”
  • Sentence 3 is OK.
  • Sentence 4.  Medical experts have long assumed that any bacteria found in the organ must have been picked up when it passed through the vagina after delivery.  Sure – some “experts” have assumed this.  But there has been growing evidence for many years that this is a bad assumption.  

I could go on and on.  Actually though I won’t.  Becuase every news story can have some limitations.  I don’t like inaccurate statements but it is a part of life I guess.  But the part that drives me batty in this story is the inclusion of a discussion about oral health.  Here are the two paragraphs that are the crux of my concern (with bold emphasizing the worst parts).

Surprisingly, the mix of bacteria in the placenta looked more like the microbiome in an adult human’s mouth than the vaginal, skin, gut, or other body microbiomes, Aagaard’s team reports today in Science Translational Medicine. The researchers think the microbes may get to the placenta from the mother’s mouth through her bloodstream, perhaps when she brushes her teeth and dislodges them into the blood. That possibility is intriguing, because there’s a well-known correlation between gum disease and preterm birth. Indeed, the array of bacteria in the placenta differed in women who gave birth early, before 37 weeks. 

“This reemphasizes the importance of oral health” during pregnancy, Aagaard says. In fact, women may need to pay attention to their teeth even before they may become pregnant, because the placenta develops early in pregnancy, she says. That may be a challenge for low-income women who can’t afford dental care, Aagaard adds. The team also found a correlation between the composition of the placental microbiome and urinary tract infections, which suggests that such illnesses or antibiotics taken to treat them could alter the microbiome in unhealthy ways.

I have read and reread the paper (which I note – is not open access – making it hard to the public to actually dig into the paper if they wanted to).  And I see no evidence presented anywhere of the importance of oral health or any causal connection between oral health and the placental microbiome or risks to pregnancies. The claims made about this here in this news story are irresponsible.  Yes, there have been some other studies about dental health and birth issues.  But nothing in this paper.  And to imply otherwise is misleading at best.  And then to go on with “That may be a challenge for low-income women who can’t afford dental care” is really not appropriate.  And to then go on about UTIs and how treating them may “alter the microbiome in unhealthy ways” is also misleading and not supported.  
Where is the critical evaluation of such claims?  Certainly the paper is very interesting.  Among the findings of interest to me: (1) that low amounts of DNA from diverse microbes is found even in the placentas from healthy pregnancies and (2) that in their analysis these microbes were most similar to those from the mouth.  But how we get from those findings (and some others) to “the importance of oral health during pregnancy” and “such illnesses or antibiotics could alter the microbiome in unhelathy ways” is, well, not in the realm of scientific research.  This is in the realm of speculation.  And speculation is fine -IF YOU TELL PEOPLE YOU ARE SPECULATING.  If you don’t tell people you are speculating I have another term for it – it is called misleading.  I assume the researchers and reporter did not intend to be misleading but that is the end result of excessive speculation without making it clear what one is doing.

Now this brings me to other articles about this study.  There are many out there.  And most seem to have eaten up this oral health connection without questioning it.  For example, consider the artilce in the New York Times yesterday:Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com by Denise Grady.  Some issues I have with this article:

  • Let’s start with the title “Study Sees Bigger Role for Placenta in Newborns’ Health.”  Well, no – there was nothing in this study that showed any evidence about a new connection between the placenta and newborns’ health.  
  • NYTimes: “During pregnancy, the authors of the new study suspect, the wrong mix of bacteria in the placenta may contribute to premature births.” Sure – they suspect it.  Would have been good to point out they have no evidence for this.
  • NYTimes: Although the research is preliminary, it may help explain why periodontal disease and urinary infections in pregnant women are linked to an increased risk of premature birth.  Again, may help explain – sure.  But it also may have no connection whatsoever.  There is no evidence presented in the paper connecting periodontal disease and UTIs and the placental microbiome.  So this is pure speculation.  And it should have been met with some discussion of all the other ways that periodontal disease and UTIs could lead to risk of premature birth.  Like leading to increased inflammation in the mother.  Or affecting blood flow in the mother.  Or other things.  There is actually a TON of research in this area.  Below are some of the factors that affect preterm labor, as listed by the Mayo Clinic – are we now discounting the years and years of work on this and going whole hog into proposing a new cause without any evidence?
    • Previous preterm labor or premature birth, particularly in the most recent pregnancy or in more than one previous pregnancy
    • Pregnancy with twins, triplets or other multiples
    • Certain problems with the uterus, cervix or placenta
    • Smoking cigarettes, drinking alcohol or using illicit drugs
    • Certain infections, particularly of the genital tract
    • Some chronic conditions, such as high blood pressure and diabetes
    • Being underweight or overweight before pregnancy, or gaining too little or too much weight during pregnancy
    • Stressful life events, such as the death of a loved one
    • Domestic violence or any form of abuse during pregnancy
    • Multiple miscarriages
    • Red blood cell deficiency (anemia), particularly during early pregnancy
    • Too much amniotic fluid (polyhydramnios)
    • Pregnancy complications, such as preeclampsia
    • Vaginal bleeding during pregnancy
    • Presence of a fetal birth defect
    • Little or no prenatal care
    • An interval of less than six months since the last pregnancy
    • Also, having a short cervical length or the presence of fetal fibronectin — a substance that acts like a glue between the fetal sac and the lining of the uterus — in your vaginal discharge might be linked to an increased risk of preterm labor. 
  • I note – the authors even say in their paper “Although this study is not able to address the relationship between periodontal disease and the placental microbiome, we, as a community of obstetricians, have appreciated for decades the association between periodontal disease and preterm birth”. Clearly the paper received more scrutiny that the quotes and the news stories. 
  • NYTimes: The new study suggests that babies may acquire an important part of their normal gut bacteria from the placenta. No.  Nothing in this study showed any connection between what is in the placenta and what is in the babies guts.  None.
  • NYTimes: If further research confirms the findings, that may be reassuring news for women who have had cesareans. Some researchers have suggested that babies born by cesarean miss out on helpful bacteria that they would normally be exposed to in the birth canal.  Again – there is no evidence that babies pick up microbes from the placenta.  So speculating that this may reassure women who have C- sections is way way way too premature.
  • NYTimes: “I think women can be reassured that they have not doomed their infant’s microbiome for the rest of its life,  said Dr. Kjersti Aagaard.  Wow. Now we have gone from “if further research confirms” to just flat out reassuring women who have had C-sections that there are no effects on the microbiome.
  • NYTimes: “It didn’t make a whole lot of sense to us,” she said. “It’s not like babies are hanging out in the vagina. They come shooting out pretty fast.” Also, she said, they emerge covered in a waxy substance called vernix, which most likely helps keep bacteria from latching on. Wow.  So babies come shooting out of the vegina and therefore cannot get microbes from the vagina.  This despite the massive amounts of evidence that they in fact do get microbes from the vagina and that C-section born babies get a different community (see for example this).  (UPDATE 5/26 – see UPDATE below with some comments / papers about C-sections vs. vaginal birth and how my use of “massive” here may be an overstatement itself).
I could go on and on.  But I won’t.  I am pleased the reporter talked to Martin Blaser who puts some damping on the speculation:

Dr. Martin J. Blaser, director of the human microbiome program at NYU Langone Medical Center, and the author of a recently published book, “Missing Microbes,” said that Dr. Aagaard’s study was important, but preliminary, and that it did not provide information that could be used in treating pregnant women. 

Thank you Martin.  But even with this, these articles leave me very frustrated.  The best I can do I guess is give out an award or two. So, for their reporting on the topic I am giving Denise Grady of the New York Times and Jocelyn Kaiser of Science News an Overselling the Microbiome award since they oversell the potential connection between oral health and infant health as mediated by the placenta.  And I am also giving this award to  Kjersti Aagaard, the first author of the paper, for her comments on the topic.

For more examples of “Overselling the Microbiome” awards see my page here.

UPDATE: Some other news stories where the headline alone is painful

UPDATE 2: Some articles that discussed placental microbes before this story came out

and many more

UPDATE 3: Paper on placental – mother – infant connection not even mentioned

Just found this paper from a Google Scholar search:  Probiotics Modulate Host-Microbe Interaction in the Placenta and Fetal Gut: A Randomized, Double-Blind, Placebo-Controlled Trial.  Seems like it is of direct relevance.  Abstract is below;

Abstract
Background: Early host-microbe interaction provides important maturational stimuli for the developing immune system. The role of prenatal microbial contact remains elusive. Objectives: Our aim was to investigate whether microbes in placenta or amniotic fluid affect fetal innate immune gene expression during late pregnancy and whether innate immune gene expression profiles in the placenta and the fetal gut may be modulated by dietary supplementation with specific probiotics. Methods: Altogether 43 pregnant women were randomized to receive (1) Bifidobacterium lactis, (2) B. lactis in combination with Lactobacillus rhamnosus GG (LGG) or (3) placebo for 14 days before elective cesarian section at full term in a double-blind clinical trial. Bacteria in amniotic fluid and placenta were detected by quantitative (q)PCR. The expression of Toll-like receptor (TLR)-related genes in the placenta and meconium samples was assessed by qPCR. Gene expression patterns in meconium were interpreted to reflect immune physiology in the fetal gut. Results: The study was completed by 29 mother-infant pairs. Bacterial DNA was detected in all placenta samples. Microbial DNA in amniotic fluid and placenta was associated with changes in TLR-related gene expression in the fetal intestine. Maternal probiotic supplementation significantly modulated the expression of TLR-related genes both in the placenta and in the fetal gut. Conclusions: Microbial contact in utero is associated with changes in fetal intestinal innate immune gene expression profile. Fetal and placental immune physiology may be modulated by maternal dietary intervention using specific probiotics.

This paper was not mentioned or cited as far as I can tell in the current study.

UPDATE 4: This paper also seems relevant

Microbial contact during pregnancy, intestinal colonization and human disease.  Abstract:

Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host–microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host–microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host–microbe interaction to reduce the risk of disease in the child.

UPDATE 5 – more misleading quotes

  • From Time’s misleadingly named article “The New Way to Predict When Pregnant Women Will Deliver“: “By focusing on oral health, we may actually be optimizing the health of the pregnancy and limiting the risk of pre-term birth,” says Aagaard. After paying so much attention to the more obvious ways to make a pregnancy healthy, it may be time to consider the less obvious – and less visible ones
  • That quote is just so inappropriate … uggh

UPDATE 6: May 24.  Some  Made a Storify with some of the Tweets related to this post.

//storify.com/phylogenomics/overselling-the-microbiome-in-placenta-story/embed?border=false&template=slideshow//storify.com/phylogenomics/overselling-the-microbiome-in-placenta-story.js?border=false&template=slideshow[View the story “Overselling the microbiome in placenta story” on Storify]

UPDATE 7: May 26 – some other papers of relevance to birth mode and infant microbiomes and placentas

A key question to me I guess is the following – how do differences between the microflora in babies born by C-Section vs. vaginal birth arise if the microbes in placentas have a big role in colonizing infants?  Perhaps the differences between C-section babies and vaginal birth babies are small — I do not know — need to dig into this more.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

"Scientific Pride and Prejudice" in the @nytimes makes claims about sciences not using evidence correctly; alas no evidence presented

Well, I guess I can say I was not pleased to see this tweet from Carl Zimmer.

//platform.twitter.com/widgets.js It is not that I have a problem with what Carl wrote. It is just that, then I went and read the article he referred to: Scientific Pride and Prejudice in the New York Times By Michael Suk-Young Chwe. And it just did not make me happy. I reread it. Again and again. And I was still unhappy.

What bugs me about this article? Well, alas, a lot. The general gist of the article is that “natural” scientists are not aware enough of how their own preconceptions might bias their work. And furthermore that literary criticism is the place to look for such self-awareness. Well, interesting idea I guess but alas, the irony is, this essay presents no evidence that literary criticism does better with evidence than natural science. Below are some of the lines / comments in the article that I am skeptical of:

  • “Scientists now worry that many published scientific results are simply not true.”
  • “Scientists, eager to make striking new claims, focus only on evidence that supports their preconceptions. Psychologists call this “confirmation bias. We seek out information that confirms what we already believe. ”
    • This statement is misleading. Confirmation bias according to all definitions I could find is something more subtle. For example Oxford Dictionaries defines it as “the tendency to interpret new evidence as confirmation of one’s existing beliefs or theories.” That is, it is a tendency – a leaning – a bias of sorts.
    • I would very much like to see evidence behind the much more extreme claim of this author that scientists focus “only on evidence that supports their preconceptions”. 
    • In my readings of actual research on confirmation bias I can find no evidence to this claim. For example see the following paper Confirmation bias: a ubiquitous phenomenon in many guises. which states:
    • As the term is used in this article and, I believe, generally by psychologists, confirmation bias connotes a less explicit, less consciously one-sided case-building process. It refers usually to unwitting selectivity in the acquisition and use of evidence. The line between deliberate selectivity in the use of evidence and unwitting molding of facts to fit hypotheses or beliefs is a difficult one to draw in practice, but the distinction is meaningful conceptually, and confirmation bias has more to do with the latter than with the former.

    • “Despite the popular belief that anything goes in literary criticism, the field has real standards of scholarly validity”
      • This is a red herring to me. I can find no evidence that their there is a popular belief that “anything goes” in literary criticism. So the author here sets a very low bar and then basically any presentation of standards is supposed to impress us.
    • “Rather, “the important thing is to be aware of one’s own bias.”
      • The author then goes on to discuss how those in the humanities are aware of the issues of confirmation bias and rather than trying to get rid of it, they just deal with it, as implied in the quote.
      • The author then writes “To deal with the problem of selective use of data, the scientific community must become self-aware and realize that it has a problem. In literary criticism, the question of how one’s arguments are influenced by one’s prejudgments has been a central methodological issue for decades.“
      • Again, this implies that scientists have not been thinking about this at all which is just wrong.
    • And then the author uses the Arsenic-life story as an example of how scientists suffer from “confirmation bias.”  If you do not know about the arsenic life story see here.  What is the evidence that this was “confirmation bias“?.  I think more likely this was a case of purposeful misleading, overhyping, and bad science.  
    • Then the author gives as an example of how science actually is prone to confirmation bias by presenting a discussion of Robert Millikan’s notebooks in relation to a classic “oil drop” experiment.  Apparently, these notebooks show that the experiments got better and better over time and closer to the truth.  And in the notebooks Millikan annotated them with things like “Best yet – Beauty – Publish”.  And then the author concludes this means “In other words, Millikan excluded the data that seemed erroneous and included data that he liked, embracing his own confirmation bias.”  I don’t see evidence that this is confirmation bias.  I think better examples of confirmation bias would be cases where we have now concluded the research conclusions were wrong.  But instead, Millikan was and still is as far as I know, considered to have been correct.  He won the Nobel Prize in 1923 for his work.  Yes, there has been some criticism of his work but as far as I can tell, there is no evidence that he had confirmation bias. 
    • I am going to skip commenting on the game theory claims in this article.
    • Then the author writes “Perhaps because of its self-awareness about what Austen would call the “whims and caprices” of human reasoning, the field of psychology has been most aggressive in dealing with doubts about the validity of its research.”  Again – what is the evidence for this? Is there any evidence that the field of psychology is somehow different?
    I could go on and on.  But I won’t.  I will just say one thing.  I find it disappointing and incredibly ironic that an article that makes claims about how some fields deal better with evidence and conformation bias than other fields does not present any actual evidence to back up its claims.  And many of the claims pretty clearly run counter to available evidence.

    UPDATE 9:20 AM 2/2/2014: Storify of discussions on Twitter

    //storify.com/phylogenomics/discussion-of-scientific-pride-and-prejudice-and-m/embed//storify.com/phylogenomics/discussion-of-scientific-pride-and-prejudice-and-m.js[View the story “Discussion of “Scientific Pride and Prejudice” and my response to it” on Storify]
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Is the New York Times microbial diversity centric?

    The answer to the question in the title – I think – is yes.  Here are some recent stories in the Times on topics of relevance to microbial diversity.

    Plus – of course – there is a continuous stream of information on microbes from Carl Zimmer who writes frequently for the NY Times.  Perhaps the best example of this is his coverage of the Human Microbiome Project papers: Studies of Human Microbiome Yield New Insights June 18, 2012.  But there have been and I am sure will be others. 
    Sure – the NY Times is not the only place with a bunch of stories about microbial diversity and microbiomes. But they do seem tto have a good ratio of “diversity” themed coverage vs. germoophobia themed topics which are common in many other places.
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    SimplyThick food thickener, necrotizing enterocolitis, and microbiomes

    Wow.  I have not heard anything about this issue until this NY Times article: Warning Too Late for Some Babies – NYTimes.com.  The article summarizes some recent FDA and other medical warnings about a product called SimplyThick.  This product has been connected to cases of necrotizing enterocolitis (NEC) in premature infants.  NEC is a horrible horrible ailment with an incredibly high death rate.  I am familiar with NEC mostly because some colleagues at UC Davis are involved in clinical trials to use probiotics and prebiotics as a preventative therapy for NEC (see more on the project here: Premie NEC — Foods For Health Institute and UC Davis Medicine – Helping Premature Infants Thrive).  NEC seems to have some general connection to “microbiome health” although it is not entirely clear (to me at least) whether the connection is correlative or causal in any way.  The NY Times article simple serves to remind me that we seem to know very very little about the connection between diet and general microbe-related health in infants (or for that matter, adults).  We desperately need to accelerate the pace at which we determine / study how foods, food additives, and diet affect our microbial communities …

    Lesson of the week from this article is captured in this quote

    “You try not to put anything in a baby’s intestine that’s not natural.” If you do, he added, “you’ve got to have a good reason.”

    I am not by any means convinced that everything has to be “natural” (I am not sure I even know what that means) but stuffing preemies full with some food thickener simply because it has been marketed to speech pathologists as something to use seems like a pretty bad idea.

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Twisted tree of life award #14: @nytimes and Nathaniel Rich on Immortal Jellyfish

    Well, this article by Nathaniel Rich in today’s New York Times Magazine certainly has gotten people talking: Can a Jellyfish Unlock the Secret of Immortality? – .  Alas, from a scientific point of view there are numerous problems with it.  So many that Paul Raeburn at the Knight Science Journalism Tracker at MIT has published a major takedown: First we get proof of heaven; now the secret of immortality. 
    Now, the science about immortality in the article is certainly bad.  But that is not what I am here to discuss.  I am here to discuss the parts of the article about evolution.  I suppose if I had read the article online instead of in print I might have been attuned already to potential evolution problems from the correction on the first page

    This article has been revised to reflect the following correction:
    Correction: November 29, 2012
    An earlier version of this article misstated the title of Charles Darwin’s classic book on the subject of evolution. It is “On The Origin of Species,” not “On the Origin of the Species.”

    Oops.  Not a good start.  The article has a lot of background about jellyfish and in particular on person who is studying them and claiming this one species is immortal (which it is not).  It is the higher vs. lower organism meme that drives me crazy in the article:

    Today the outermost twigs and buds of the Tree of Life are occupied by mammals and birds, while at the base of the trunk lie the most primitive phyla — Porifera (sponges), Platyhelminthes (flatworms), Cnidaria (jellyfish).

    And then 

    The mystery of life is not concealed in the higher animals,” Kubota told me. “It is concealed in the root. And at the root of the Tree of Life is the jellyfish. 

    Seriously?  The root of the tree of life is the jellyfish?  And higher vs. lower organisms?  What exactly is a higher organism?  Does this mean that jellyfish have not evolved since their branch separate from the trunk of the animal tree?  Oh – and – what about the rest of the Tree of Life – you know – outside of animals for example?  Aaargh.  
    The higher vs. lower meme continues with this quote:

    Hydrozoans, he suggests, may have made a devil’s bargain. In exchange for simplicity — no head or tail, no vision, eating out of its own anus — they gained immortality.

    Really?  So there is a tradeoff between complexity and immortality?  So does this mean all simple organisms are more immortal?  And all complex ones are doomed?  Where does this notion even come from?
    For helping perpetuate the higher vs. lower organism meme (which drives me batty) I am awarding the author and the editor and the NY Times my coveted “Twisted Tree of Life” award.

    As an aside, the article is littered with painful other statements like

    It is possible to imagine a distant future in which most other species of life are extinct but the ocean will consist overwhelmingly of immortal jellyfish, a great gelatin consciousness everlasting.

    So – this jellyfish operates in the absence of an ecosystem?  Suppose individual organisms are “immortal” as claimed in the article.  What exactly will they eat when everything else is gone?
    Plus there is a conspiracy part that is lame.

    You might expect that biotech multinationals would vie to copyright its genome; that a vast coalition of research scientists would seek to determine the mechanisms by which its cells aged in reverse; that pharmaceutical firms would try to appropriate its lessons for the purposes of human medicine; that governments would broker international accords to govern the future use of rejuvenating technology. But none of this happened.

    Really?  So all the scientists and companies of the world have ignored this amazing finding?  Maybe, just maybe you might think that is because this is BOGUS?
    And then there is the bogus “small bodied organism” problem.

    He cited this as an example of a phenomenon he calls the Small’s Rule: small-bodied organisms are poorly studied relative to larger-bodied organisms. There are significantly more crab experts, for instance, than hydroid experts.

    What?  Is this even remotely serious?  So ignore Drosophila as a model for animals.  Or mice for that matter.  Ignore Arabidopsis as a model for plants.  Ignore yeast too.  And E. coli.  Uggh.  Completely inane. 
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Velasquez-Manoff opinion piece in the NY Times on autism, parasites & inflammation; nice ideas; not enough caveats

    There is a very interesting “Opinion” piece in the New York Times today: Immune Disorders and Autism – NYTimes.com.  By Moises Velasquez-Manoff is details some recent work that the author believes relates to autism and a variety of other human ailments with an autoimmune connection.

    The general logic/key points seem to be as follows:

    • Some autism cases look like a form of inflammatory diseases with the immune system overactive (inflammation on high, anti-inflammation on low, or some combination thereof)
    • Infection of a mother during pregnancy increases the risk of having a child with autism.
    • In animal models, inducing inflammation in the mother (even without an infection) leads to an increased risk of behavioral “problems” in her offspring
    • Inflammatory and/or autoimmune diseases (e.g., asthma) have increased in incidence along with autism.
    • If a mother has automimmune or inflammatory diseases such as rheumatoid arthritis celiac disease she has a higher risk of having a child with autism.  Similarly if a mother has allergies or asthma during the second trimester, there is a higher risk of having children with autism.  
    • Many automimmune and inflammatory disorders and autism are all more prevalent is the developed world.
    • The developed world is generally cleaner that the developing world.  
    • There are many fewer parasites in people in the developed world.
    • Parasites are known to suppress inflammation.
    • Therefore, we may be able to stop/limit autism, asthma, and other inflammatory diseases by purposefully infecting people with parasites from our evolutionary past. 

    Now, personally, I like the general hypothesis here.  It makes complete sense.  But alas, it is suffers from this issue that is spreading almost as fast as these diseases – a lack of a discussion of the distinction between correlation and causation.  I have been obsessing about this a bit recently with studies of the microbiome.   Overall, I do like this current article.  It mixes human epidemiological studies with controlled animal studies with discussion of conceptual models.  But alas there is really no discussion of the challenges if disentangling correlations vs. causation. And I think it is a bit dangerous in the latter parts with the jump to potentially curing these various ailments by purposeful infection with parasites.  Again, I like the idea.  But a few caveats would have been nice.  I am glad it was marked as an opinion piece but even when one states an opinion about a medical issue, one can still say “there are reasons why this might not be true .. such as …”.  Too bad that wasn’t done here.

    UPDATE – Emily Willingham has written a VERY detailed critique of the article that I think everyone interested in anything related to this topic should read: Emily Willingham: Autism, immunity, inflammation, and the New York Timeswww.emilywillinghamphd.com.

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    For those interested … storification of twitter discussion criticizing NY Times article on Venter cell model

    Storification is here and below.
    http://storify.com/phylogenomics/critiques-of-ny-times-story-on-venter-cell-model.js[<a href=”http://storify.com/phylogenomics/critiques-of-ny-times-story-on-venter-cell-model” target=”_blank”>View the story “Critiques of NY Times story on Venter Cell Model” on Storify</a>]

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    If you subscribe to the NY Times – you might want to cancel to get their secret discount

    Just got this email

    Dear New York Times Reader, 


    You may have received an e-mail today from The New York Times with the subject line “Important information regarding your subscription.” 


    This e-mail was sent by us in error. Please disregard the message. We apologize for any confusion this may have caused. 


    Sincerely,


    The New York Times

    Which then caused me to go back to my trash and read the previous one:
    Dear Home Delivery Subscriber, 

    Our records indicate that you recently requested to cancel your home delivery subscription. Please keep in mind when your delivery service ends, you will no longer have unlimited access to NYTimes.com and our NYTimes apps. 

    We do hope you’ll reconsider. 

    As a valued Times reader we invite you to continue your current subscription at an exclusive rate of 50% off for 16 weeks. This is a limited-time offer and will no longer be valid once your current subscription ends.* 

    Continue your subscription and you’ll keep your free, unlimited digital access, a benefit available only for our home delivery subscribers. You’ll receive unlimited access to NYTimes.com on any device, full access to our smartphone and iPad® apps, plus you can now share your unlimited access with a family member.† 

    To continue your subscription call 1-877-698-0025 and mention code 38H9H (Monday–Friday, 8:30 a.m. to 8:30 p.m.; Saturday, 9 a.m. to 3 p.m. E.D.T.). 

    This is a service message. You are receiving this e-mail to confirm your New York Times home delivery cancellation. 

    *This 50% promotional offer is available for the first 16 weeks. At the end of this promotional period, delivery will continue at the regular rate unless you notify us otherwise. You will be billed or your credit card automatically charged in advance of each 4-week billing period. This offer is valid only in areas served by The New York Times Delivery Service. Prices are subject to change. Offer is subject to additional restrictions or limitations. State and local taxes will be added where applicable. Product availability and price may vary by region. This is a limited-time offer and will no longer be valid once your current subscription ends. Offer is not transferable and is only available to the recipient of this e-mail.

    †Mobile apps are not supported on all devices. Does not include e-reader editions, Premium Crosswords or The New York Times Crosswords apps. Book Review and Large Print Weekly subscriptions do not include All Digital Access. Other restrictions apply. 

    So apparently if I had cancelled my subscription I would be able to get a temporary discount to restart my subscription.  Well, that is interesting.  Gonna be canceling my subscription soon I think …
    I note – despite the generally excellent writing at the NY Times I am a bit perplexed by the signature suggesting this email was actually coming from the newspaper and not a person in the circulation department …
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–