Tony Rodriguez Illustration of Me for WiredUK

OK so I have not worn a tie in a very long time and I pretty much don’t wear a lab coat too often either but I totally love this:

// See the whole story here.

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

 Here is the full text of my responses:

“got asked by another reporter to comment on this

so – have seen the paper 

it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). “

I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 

Without seeing the alignments I offer multiple alternative hypothesis for their findings

  1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note – clustalw is a bit notorious for not producing idea alignments in some cases.
  2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
  3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
  4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
  5. Related to alignments they need to show which regions of alignments they excluded from phylo
  6. Convergent evolution could also explain some of the patterns they observe.
  7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.

Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate – I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.

Reporter asking what other analyses could they do

So – I don’t want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 

In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.

Reporter asking about initial impressions:

I see little here that is particularly convincing evidence for HGT …

My follow up email

Note – I am not saying that this is a bad paper — just that I am not overwhelmed by their evidence and especially by what they put in the paper. 

For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don’t see how they tested alternative hypotheses …

Some related links:

Also here are some presentations from many years ago with some discussion of HGT

Quick ego-post – link to interview of me by National Geographic Weekend show

Quick post here.  Was interviewed for National Geographic Weekend by Boyd Matson a few days ago and the show was just posted online: January 19, 2013: Waging War Against Whalers, Paragliding Above Pakistan and More – News Watch.  Scroll down to find the link to my part ..

Yes, the human microbiome has truly arrived: on Wait Wait Don’t Tell Me

So cool.  Yesterday on “wait wait … don’t tell me” Kai Penn (actor) was enticed to play the game “Ahhh! Get It Off Me!” in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.


The evil germy pacifier story is getting out of hand – w/ Dr. Glass misleading the charge

From Wikipedia

Oh for crying out loud.  This is getting out of control.  Two weeks ago I wrote about an over the top story in US News and World Report about pacifiers and microbes: The Tree of Life: Germophobia 101: there are microbes on pacifiers ….  The culprit in this story was a Dr. – Dr. Tom Glass – who was the lead presenter of some study at a meeting.  His study involved counting the number of colony forming units on used vs. new pacifiers.  And low and behold used ones were covered in germs.  Amazingly, this led Glass to say ridiculous things like

In the long run, it may be that what you do now [using a pacifier] may have a lot to do with whether a child ends up developing atherosclerosis or type 2 diabetes.

Completely misleading and deceptive and dangerous I would say.  And alas, the story has been crawling it’s way around the web picking up speed.  Now it is at Time.Com with another story about Glass’ work: Bacteria on Binkies: A Recipe for Crankiness |  Glass apparently is now blaming biofilms of pacifiers for all the problems.  And again Dr. Glass is (mis)leading the charge against pacifiers.

A lot of times when a child is cranky, the first thing a parent does is reach for a pacifier,” says Dr. R. Tom Glass, the study’s principal investigator and a professor of forensic sciences, pathology and dental medicine at Oklahoma State University. “But what are you using to treat the crankiness? It’s a vicious cycle.


“biofilms can potentially increase the likelihood of colic or ear infections and could possibly heighten the risk of allergies or asthma, says Glass.”

The reporter does present some skepticism from parents and from the literature.  But come one – why even report this crap from Glass.  I mean – I am all for keeping babies from getting sick and pacifiers very well may be a source of some nasties.  But let’s think about the big picture here.  Parents buy pacifier.  Parents open package.  Parents give to baby.  Baby puts in mouth.  Baby drops pacifier and it gets dirt on it as well as some germs.  Baby puts back in mouth.  Pacifier gets left on counter.  Things from babies mouth grow on pacifier.  Baby puts pacifier back in mouth.  And so on.  Tell me again where the pacifier introduces bad germs to this system?

UPDATE: some reading material

Hmm .. apparently I am not supposed to be posting about #UCDavis in "social media" (SEE UPDATE AT BOTTOM)

At the suggestion of a colleague I have been browsing through the UC Davis Policy and Procedure Manual – Chapter 310, Communications and Technology Section 40, University Communications: Publications, Graphic Standards, Marketing, and Media Relations.

Much of it is straightforward but much of it seems to basically be discouraging any direct social media posts or interaction with the press. See for example:

The News Service unit in University Communications is the exclusive source for developing and disseminating news about UC Davis to the general public via newspapers, radio, television, magazines, and the World Wide Web, including social media and related channels. The News Service unit determines the newsworthiness of significant developments and activities in academic research; administrative programs; accomplishments of faculty, staff, or students; events; and other campus matters. It conducts or coordinates direct contact with news media representatives, and assures that media relations are timely, accurate, comprehensive, and of broad public interest.


Generally, the news media will contact the News Service to find a source for a story. If a reporter contacts a source directly, that faculty member, staff member, or student shall notify the News Service

Hmm … so ..  when I was contacted by multiple reporters about the pepper spray incident and for my comments on it and on the handling of it by UC Davis I was supposed to notify the UC Davis News Service.  I suppose I could have done that.  But how about this – I communicate with dozens if not 100s of reporters on Twitter about all sorts of things.  Should I notify the news service about each contact?  That would actually be kind of fun.  They would block my emails very soon thereafter I am sure.
I am also wondering about the role of the News Service as the “exclusive source for developing and disseminating news” “via newspapers, radio, television, magazines, and the World Wide Web, including social media and related channels.”  So is this saying I am no longer supposed to write about UC Davis on social media?   No more blogging?  No more Twitter?  How does this jibe with all the retweets and reposts I get by official UC Davis groups/people?  
In the end I can imagine that the UC Davis administration would say this wording is not quite what they mean.  But it is there.  And technically, I am supposed to follow it.  Oh well, off to kill all my social media accounts.  Yeah, right.

UPDATE: Barry Shiller – UC Davis Communications Chief Guru has responded with clarifications that this policy is NOT intended to suppress any communications but is about coordination with the News Service

I’m replying directly and publicly as an expression of transparency, and professional respect for you.

You indeed misinterpret the policy. It was, and is, intended to optimize coordination with the media – not, as is inferred by your post, to inhibit anyone. Coordination, by the way, is as beneficial to the media as anyone. They appreciate knowing their go-to points of contact. That said, reporters contact faculty, staff and students without interference or inhibition. All the time. 

It may be that this policy fails to clarify or contemporize the distinction between “reporters” and social media content creators, including bloggers. If so, we will take a look at it; I’d welcome your input. 

But let me be clear: as you well know, many university constituents actively blog, tweet, post, opine. (I’m among them.) In this age, it is an important ingredient in telling our story. The policy is not intended to discourage that

Fungal parasite of caterpillars is source of "Himalayan viagra"

Photo by Nicolas Merky

Wow – never heard of this fungus before reading this CNN piece: ‘Himalayan Viagra’ taking its toll on Nepal – The fungus infects caterpillars (larva of a ghost moth) in the Himalayas and kills them. And the fungal coated dead caterpillars are, alas, considered to have multiple uses in various traditional Chinese medicine practices. One of the uses is as an aphrodisiac and thus these have become known as “Himalayan viagra”.

The fungus that does this is Ophiocordyceps sinensis – (it is an Ascomycota).  Not a huge literature out there if you search just for this species name but thanks to Wikipedia I found out there are some synonyms so if you search Pubmed for all the names one gets 328 papers and 56 of these have free full text including a few that seem quite useful:

So – seems that what happens here is the fungus infects larva and then kills them and then a fruiting body grows out of the caterpillars head … fun.
Snooping around led to some other news stories about this system including many that came out recently
Anyway – seems like this would be a fun organism for genome sequencing … 

For those who missed it: "Science as an open enterprise" from Royal Society

This will be of interest to many I think: Science as an open enterprise – Report | Royal Society

It is a comprehensive report from the Royal Society with links to videos, text, previous meetings, references, EPUBs, and more relating to a report that was released a few days ago.  From the web site:

Six key areas for action are highlighted in the report:

  • Scientists need to be more open among themselves and with the public and media
  • Greater recognition needs to be given to the value of data gathering, analysis and communication
  • Common standards for sharing information are required to make it widely usable
  • Publishing data in a reusable form to support findings must be mandatory
  • More experts in managing and supporting the use of digital data are required
  • New software tools need to be developed to analyse the growing amount of data being gathered

Definitely worth a serious browsing/reading.

For more on this see …

Go PLOS Biology – getting lots of press coverage for recent pubs

Just got this email from PLoS Biology and thought I would share – it has links to press coverage of recent PLoS Bio papers  :

We are writing to update you on some papers recently published in PLoS Biology.This is a summary of our recent media coverage for PLoS Biology board members, friends, and for editors. Thank you again for your support of the journal.

On January 3, PLoS Biology published an article by Prof. Alex Rogers et al., which detailed a survey of Antarctic waters along the East Scotia Ridge in the Southern Ocean, revealing a new vent biogeographic province among previously uncharacterized deep-sea hydrothermal vent communities. This received significant coverage in the media, a selection of which is below:

The New York Times
The Guardian
Washington Post

PBS News Hour (video)
BBC World Service (audio)
Press Association
Discovery News
Reuters (video)
The Telegraph
Scientific American
National Geographic
ABC (Australia)
Sydney Morning Herald
CBC (Canada)
Fox News
New Scientist
The Mirror
The Daily Mail
Indian Express

In the same issue, PLoS Biology published an article by Dr David Ornitz and colleagues, which described how FGF20 signaling in mice is required specifically for the differentiation of cochlear outer hair cells – the cells most often damaged during age-related hearing loss. This also received attention in the media, including the following:

NHS Choices
Press Association
The Mirror
The Daily Mail
Irish Examiner