Thursday, April 04, 2019
The Twisted Tree of Life Awards and Why We Should Care About Misrepresentations of the Tree of Life
I will be posting a lot of notes about the talk soon but wanted to get at least some of the main material down here for people to look at if they are interested.
Screencapture video with Audio
Some Tweets about the Talk Twisted Tree of Life Awards talk for #Nelli19
Saturday, March 23, 2019
Blog post w/ Twitter thread about Twitter threads & blog posts & how to turn a Twitter thread into a blog post
But that was not the only Tweet I made about this. I made a whole frigging thread. You can see the thread in most Twitter clients by clicking on the Tweet. But I figured I would also capture the thread here in this blog post. Tweet #2 in the thread.So @PatSchloss had a Tweet a few minutes ago about a comment he got suggesting Twitter threads are more effective than blog posts and I thought I would comment about this in a thread 1/n https://t.co/WxHXyFTZOS— Jonathan Eisen (@phylogenomics) March 23, 2019
Tweet #3 in the Thread.I think this is only partially true. In the short term and for most purposes, Twitter threads are probably more effective. 2/n— Jonathan Eisen (@phylogenomics) March 23, 2019
Tweet #4 in the Thread.But Twitter threads mostly seem to get lost / ignored after a short period of time (days) 3/n— Jonathan Eisen (@phylogenomics) March 23, 2019
Tweet #5 in the Thread.Blog posts on the other hand have longer legs and also have the advantage in most cases of being updatable and more able to accommodate different formats and such 4/n— Jonathan Eisen (@phylogenomics) March 23, 2019
Note - I got the embed codes for these Tweets from Twitter by selected the drop down menu in the upper right of the Tweet which I see in Safari at the Twitter site. I am not sure if this shows up in all Twitter clients but it works on the Twitter web site.So what I have started doing in some cases is posting Twitter threads and then capturing them via @wakelet or embeds into a blog post with some other details and this then has a bit longer lifespan than the thread itself. 5/n— Jonathan Eisen (@phylogenomics) March 23, 2019
This gets me this menu
I then selected "Embed Tweet" and it gives me this
I then selected customization options because when posting all the Tweets I wanted just the Tweets and not the full conversation of the Tweet. First you get this menu:
I then selected "Hide Conversation"
And clicked update and then it showed me the new Embed code. I then copied it and inserted it into this blog post. I did this for each of the five tweets shown above.
And Voila - I have a blog post with a Twitter thread embedded in it where the thread discusses blog posts vs. Twitter threads.
Also - one can also include other Tweets about the same topic here. So for example I can include responses too ...
Like this one.
Yes. I have a blog post I’ve given to 100+ people over they past few years. Tweets are pretty ephemeral. https://t.co/nc6fVcCmqw— Pat Schloss (@PatSchloss) March 23, 2019
If a thread is long, this is a real pain. A much easier though less controllable approach is to use Wakelet or Twitter moments. However, since Twitter seems to be abandoning moments as far as I can tell, Wakelet seems a better option
Here is the Wakelet I made --- Anyhow - there you go. A quick guide to turning a Tweet thread about blog posts and Tweet threads into a blog post.
The place is: https://www.inaturalist.org/places/rural-areas-between-davis-and-woodland
Friday, March 15, 2019
So in 2011 I won this award called the "Benjamin Franklin Award for Open Access in the Life Sciences. " I was happy about it at the time. I got a book and a plaque and was toasted at a meeting in Boston. A few years ago I and others noted that the award had been given only to men. Then Helen Berman won the award in 2014 and it looked like maybe the process was starting to not be so biased.
But I got alerted to the ongoing issues again by an email a few days ago. And not only have the other winners all been men, all four nominees this year are men too.
- 2002 – Michael B. Eisen
- 2003 – James Kent
- 2004 – Lincoln D. Stein
- 2005 – Ewan Birney
- 2006 – Michael Ashburner
- 2007 – Sean Eddy
- 2008 – Robert Gentleman
- 2009 – Philip E. Bourne
- 2010 – Alex Bateman
- 2011 – Jonathan A. Eisen
- 2012 – Heng Li
- 2013 – Steven Salzberg
- 2014 – Helen M. Berman
- 2015 – Owen White
- 2016 – Benjamin Langmead
- 2017 – Rafael Irizarry
- 2018 – Desmond Higgins
When I won the award I was happy but I did notice the gender bias of the winners although that was when I was kind of just waking up to the issue of gender bias in STEM. I tried to get people to nominate more women for the award the next year via FriendFeed, Twitter, email and other means. For example:
2012 Franklin Award Accepting Nominations - please consider nominating women - all past winners incl. me are male http://t.co/8DLeiPp6— Jonathan Eisen (@phylogenomics) February 17, 2012
2012 Franklin Award Accepting Nominations - please consider nominating women - all past winners incl. me are male http://t.co/8DLeiPp6— Jonathan Eisen (@phylogenomics) February 17, 2012
Here is the summary:
The selection process
- Nominations may be submitted by members of Bioinformatics.org using this form (you must be a member and logged in).
- Any person may be nominated, but the final list of nominees will be determined by Bioinformatics.org, based on the following criteria:
- All nominations must be submitted by current members of Bioinformatics.org.
- Self-nominations will not be counted.
- Nominations of past laureates will not be counted.
- There must be evidence that the nominee has done something to promote open access in the life sciences.
- After the above exceptions have been considered, there must remain at least two (2) nominations per nominee (a member must ``second'' each nomination).
And since the Ben Franklin award is basically only for men, it seemed inappropriate to have my plaque for the award hanging up, especially just below my "Everyone Needs Feminism" sign, so I took it down #GenderBias #STEMDiversity pic.twitter.com/DgxdgAIC3o— Jonathan Eisen (@phylogenomics) March 18, 2019
Sunday, March 10, 2019
Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500
I went to West Sacramento, to a pond there, to see, and hopefully take pictures of, a garganey. What, you ask, is a garganey? It is a kind of duck. According to Wikipedia:
The garganey (Spatula querquedula) is a small dabbling duck. It breeds in much of Europe and western Asia, but is strictly migratory, with the entire population moving to southern Africa, India (in particular Santragachi), Bangladesh (in the natural reservoirs of Sylhet district) and Australasia in winter, where large flocks can occur. This species was first described by Linnaeus in 1758. Like other small ducks such as the common teal, this species rises easily from the water with a fast twisting wader-like flight.
So - kind of boring in some sense. Just another duck right? But the key for my outing today is that it is not a normal resident of Wast Sacramento, or Central California, or California, or North American even. It is, as my National Geographic bird field guide says in a colonialist phrasing "An old world species"
So when one was spotted a few weeks ago in the West Sacramento area, the birders got very excited. And they started to share information about it on Facebook, and eBird (which is where I heard about it) and Twitter and such. And it even made the news: Bird Watchers Flock To West Sacramento To Catch A Glimpse Of Rare Bird
So why, you may ask, did this interest me? Well, I have been a birder, on and off, since I was a kid. Birds, and birdwatching, are what got me into nature, which then got me into natural history, which then got me into biology, which then got me to where I am now. For example, my first science job, doing field in the summer of 1988, involved studying hummingbirds in Colorado at the Rocky Mountain Biological Laboratory with Bill Calder from Arizona.
More recently, I have rediscovered birding and bird science. From a birding point of view, I got back into birding when we went on a trip to Costa Rica a few years ago. For that trip, I got my first good pair of binoculars (Leica Trinovid 8 x 42) I have ever owned. And I got my first digital SLR camera (a Nikon D80) and a nice lens (a Nikkor 70-200 f/2.8). This was a great set up to have. although I confess I never fully learned all the ins and outs of using it for photography. I mean, I used it a lot, but I never learned how to do much other than leave it on auto settings and use some of the "scene" settings to vary things up. I wrote some blog posts about birding in the area on and off too and also started to spend a lot of time in Yolo Bypass nearby Davis. See for example:
- Harvard Club of Sacramento outing to Yolo Basin #Birds #Birds #MoreBirds
- Great kids activity in Davis - the U. C. Davis Raptor Center
- Davis Wetlands - Beatiful Place, but Bizarrely Closed to Visitors most of the Winter
- Good day at Yolo Basin - Birds, Otters and more
- Vic Fazio Yolo Wildlife Area - A Stunning Place 5 Minutes from Davis
- Lab meeting at Yolo Basin - science should be fun ...
- Bat tour at Yolo Basin Wetlands
- Day 4 of the #ChallengeOnNaturePhotography - great horned owl in #Yolo Basin
- Yolo Basin 1-6 - yellowthroat, sora, and more
- Yolo Basin Notes Jan 5, 2014
- Best of #Yolo Bypass Photos
- Pictures from Yolo Basin - Bitterns, Night Herons, Owl
And I should note that I also have been going on and on and on about how microbiologists could learn a lot from birders and how I think we need a "Field Guide to the Microbes."
So, yeah, birds and birding were and are bigs parts of my life.
Anyway, back to the garganey. Why was I checking out eBird reports and following reports of bird sightings? Well, because I REALLY rediscovered birding in the last two months. This happened because after about two years of pondering, and about 1 year of serious research, I got a new camera and lens specifically to do more bird photography. In order to choose what camera to get, basically, I looked and looked and looked and finally found someone online who made recommendations for bird photography that I really trusted. This person is Mark Smith. And I found his recommendations via the oracle of Google and then watched a series of his videos on Youtube about comparing and contrasting different set ups for bird photography. Especially bird in flight photography. This had been my bane in a way. I just felt like with my current birding set up I was not able to get close enough to birds or get good pictures of them in flight. And Mark Smith's videos showed me how I could get to the next level. Based on his videos I finalized my choice to a Nikon D850 w/ a crazy fancy lens (for more than $10,000) or a Nikon D500 with a Nikkor 200-500 mm lens for about $3000. I decided on the $3000 option both to save money and because I was not sure I would really use the rig enough to justify $10K. So here is what I got, based on Mark Smith's guidance:
- Nikon D500 DSLR Camera (Body Only)
- Nikon AF-S NIKKOR 200-500mm f/5.6E ED VR Lens
- Oben GH-30 Gimbal Head
- Benro TMA47AXL Extra Long Series 4 Mach3 Aluminum Tripod
Everything showed up in early January. And I started to try to learn how to use everything. And things were slow at first. I went out for a few weeks taking pictures using auto settings. And, well, it was nice, occasionally. But the pics just were not as good as I thought they would be. It all came to a head when I went on a local little outing with Jim Koenigsaecker. And he kept asking me about all the settings I was using. And I kept saying "blarg" or something like that (actually, I said mostly I was using just the automated settings). And when I went home from that day, I had some good pics. And a lot of crummy ones.
So then I decided to consult the oracle again. Google that is. And I found Mark Smith had a bunch of videos on how to set up the Nikon D500 for shooting birds in flight
And I watched these. A few times. And then set up my camera with those settings. And I went out again that afternoon. And BOOM. The pics were way way way better.
See for example these.
Anyway - more about my pictures from the past another time. Back to the garganey. As part of taking better pictures I started wanting to share them more. And I started being able to ID birds better and in some cases also wanted help confirming IDs. So I started using iNaturalist and eBird more.
See my iNaturalist posts here.
See my eBird posts here.
And I signed up for notifications about bird sightings via eBird.
And this is FINALLY where the garganey comes in. A few weeks ago I saw that some people had reported a rare bird on eBird - a garganey. I also saw these were reported in the West Sacramento area, near the deep water channel and near where UC Davis students do crew and sailing. So this stuck in my head somewhere for a few weeks. And I talked about possibly going to check it out with some birding friends like Mei Yamaguchi. And then, a few days ago my friend from TIGR Karla Heidelberg contacted me and told me she was going to be in the Davis area this weekend since her daughter would be racing in two crew regattas. So yesterday we met up to see Captain Marvel with my wife, daughter, mom and step dad. And Karla came with her son, who it turns out, is getting interested in bird photography. And while chatting before or after the movie I asked where her daughter was going to be racing Sunday and she said "somewhere near West Sacramento".
Thursday, March 07, 2019
Kisaco Research - sponsoring YAMMMM - yet another mostly male microbiome meeting - again - not their first biased rodeo
Happening next week in Kansas City. Run by Kisaco Research. I have written about their propensity to have meetings where most of the speakers were white men previously. See
- Another white men's microbiome meeting from Kisaco #YAMMM #manel #STEMDiversity
- The White Men's Microbiome Congress #YAMMM #Manel #Boycott
Tuesday, March 05, 2019
The ad claims that Dove is gentle on the microbiome. OK. I am not sure I get what that means completely. But I think they are saying "Our product does not mess up your microbiome". I guess this could be good for some people if it were true. But for others, maybe you want to mess up the microbiome. Regardless, I would love to see data, if it exists, behind such a claim because my guess is that any body wash affects up the microbiome in many ways.
So, if they were not going to show evidence for this claim, I wondered, what are the ingredients of this Dover product? Fortunately the company provides them readily: https://www.dove.com/us/en/washing-and-bathing/body-wash/deep-moisture-body-wash.html. And here they are:
- Water (Aqua),
- Cocamidopropyl Betaine,
- Sodium Hydroxypropyl Starch Phosphate,
- Lauric Acid,
- Sodium Lauroyl Glycinate,
- Sodium Lauroyl Isethionate,
- Hydrogenated Soybean Oil,
- Glycine Soja (Soybean) Oil,
- Sodium Chloride,
- Fragrance (Parfum),
- Guar Hydroxypropyltrimonium Chloride,
- Stearic Acid,
- Citric Acid,
- Sodium Isethionate,
- Iodopropynyl Butylcarbamate (IPBC)
Phenoxyethanol is also an antimicrobial. See for example this where they report things like:
The study reveals that the six preservatives-Phenoxyethanol, Methyl paraben, Propyl paraben, Sorbic acid, Potassium sorbate and Sodium benzoate shown antimicrobial activity with the three test organisms at various concentrations and time periods.My guess is many of the other ingredients can also affect the microbiome. This would not really be surprising as lots of things affect the microbiome. So, sorry Dove, but just saying your product is "gentle on the microbiome" just does not cut it for me.
I decided to see if I could find out anything else about Dove's claim of being gentle on the microbiome so I did the usual thing and Googled "Dove microbiome" and found some of their material on the microbiome. And I guess I could say I was pretty disappointed. For example see this:Introducing your skin’s microbiome – Dove Nothing there providing data on just how gentle Dove really is or is not on the sin microbiome. And in addition there was a statement I was not so fond of:
"Think of it as an invisible eco-system that lives on the skin that’s working to help keep it healthy and in good condition. "Umm -- no -- no evidence for this. The microbes on your skin appear to mostly be working for themselves. Some of the time they are harmful. Some of the time they are helpful. Some of the time they are neither. But they are certainly not "working" to keep skin healthy.
So - it seems like Dove wants to get in on the microbiome hype. I guess I am glad they are interested in the microbiome. But they cannot just make claims about things like "being gentle" on the microbiome without evidence. Especially when their ingredient list contains a collection of known antimicrobial chemicals.
This is definitely worth a read:
Drug Companies and Doctors Battle Over the Future of Fecal Transplants - The New York Times. By Andrew Jacobs. March 3, 2019.
The lead in is good:
CAMBRIDGE, Mass. — There’s a new war raging in health care, with hundreds of millions of dollars at stake and thousands of lives in the balance. The battle, pitting drug companies against doctors and patient advocates, is being fought over the unlikeliest of substances: human excrement.The story is both interesting and includes some very important stuff going on behind the scenes that may affect the future of fecal transplants as a treatment in t. It seems that a variety of folks including those from companies who are trying to develop treatments mimicking fecal transplants are trying to get the FDA to crack down on the use of actual feces for carrying out fecal transplants.
“The first principle of medicine is do no harm, and at the moment we don’t have a long-term track record of F.M.T.’s adverse effects,” said Dr. Sahil Khanna, an associate professor of gastroenterology at the Mayo Clinic who has conducted industry-funded clinical trials on fecal transplants. “We also need to move away from transferring poo from one person to another.”and
Drug companies, which have been struggling to funnel patients into the clinical studies that are required for F.D.A. approval, would like federal officials to restrict the stool bank’s ability to distribute fecal matter in the hope that more patients will enroll in their trials.On the other side are those from places like OpenBiome as well as many clinicians who think that the regulation may have already gone far enough or even too far.
“It is very frustrating to see hyperregulation again ruining a good thing in health care,” said Dr. Colleen Kelly, a gastroenterologist at the Brown University medical school.and
“I never imagined the solution to my nightmare could be so simple,” he said. “I just hope Big Pharma doesn’t make it unaffordable for the people like me.”
Tuesday, February 26, 2019
A conference where all the speakers are women - happening this week #YAMMM #manels #STEMDiversity #GenderBias
See The Tree of Life: A conference where the speakers are all women?
I wrote about this because of the general issue with excessive numbers of conferences where most or all of the speakers were men. I had come up with a term for such meetings - YAMMM. Yet Another Mostly Male Meeting. I even made some little pics / images to represent such YAMMMs.
And I blogged and Tweeted about such meetings a lot (and still do). See STEM Diversity posts and related links here for example.
When I wrote the post I was wondering if this would be a good counter to the problem of these YAMMMs (also called manels by others). The feedback (much of it on Twitter) was really useful, mostly. And over the years I pondered doing such a thing but to be honest, never felt really comfortable with the idea. I worried about some of the possible negative sides of doing this, such as how the speakers might get unwanted attention and critiqued for being selected solely because of their gender. And I also worried about whether this would be viewed in some way as a form of "reverse discrimination".
But I did try to do other analogous things where one reversed the normal gender skew (which is almost always towards males). For example, when I found out, kind of at the last minute, I was speaking at a meeting with a very very skewed gender ratio of speakers, I gave my talk, but changed only referenced the work of women in the field. See What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)? And in a class I teach I decided to basically replace most of the white male scientists I had been referencing with women and people of color. Small things I know. But I was pleased when people noticed these efforts and commented on how it made them think a bit about the examples we use when we give talks and teach.
Mind you, I have organized or helped organize a lot of meetings and seminar series since that post six years ago. And I have tried to have the speakers at these be representative of diverse backgrounds in terms of gender, ethnicity, career stage, type of institution, and more. But I myself have never gone to the next level and flipped the standard gender bias on its head.
Thus I was intrigued in September last year when I found out that my friend and colleague Dr. Rob Knight was co-organizing (with Dr. Sandrine Miller-Montgomery) a meeting in San Diego on "microbiomes" (my main area of research) where all of the invited speakers were women. I blogged briefly about this here: 1st annual CMI International Microbiome Meeting (CIMM) w/ a great #STEMDiversity statement & plan. I include below the material from the conference site that I included in that post:
On behalf of Dr. Rob Knight, the Center for Microbiome Innovation is pleased to host the 1st annual CMI International Microbiome Meeting (CIMM) on February 27–28, 2019 in San Diego. Additionally, we are pleased to announce that the 1st Urobiome Meeting on February 26, 2019, led by Linda Brubaker MD, will occur in conjunction with CIMM to make the most of your visit to San Diego.
During the first day of this event, leading researchers will present on the emerging science of the Urobiome and its recently discovered implications for human health, including common conditions such as urinary tract infection, urinary incontinence and bladder overactivity.
The following two days will feature high-impact presentations on the latest discoveries in microbiome sciences, with sessions on topics ranging from the microbiome in human disease and wellness and the metabolome, to primate microbiomes, to environmental and ocean microbiomes. For this first edition, we have decided to demonstrate that it is possible to have a large representation of women presenters in a scientific meeting by inviting only women speakers. Be prepared to hear from fantastic presenters such as Dr. Katie Amato (Northwestern University), Dr. Rita Colwell (University of Maryland), Dr. Merete Eggesbo (Norwegian Institute of Public Health), Dr Susan Prescott (University of Western Australia), Dr. Lita Proctor (NIH), and many more!In addition, I agreed to serve on a panel at the end of the meeting discussing "Breaking the Glass Ceiling: How do we solve the gender imbalance in STEM?" (I had found out about their plans for the meetings when they invited me to serve on the panel). As someone who has critiqued meetings for egregiously skewed gender ratios of speakers and as someone who has called attention to in particular the many microbiome focused meetings with gender balance issues, the whole idea behind this conference was in essence represented by this statement:
For this first edition, we have decided to demonstrate that it is possible to have a large representation of women presenters in a scientific meeting by inviting only women speakersThis was certainly a bold move by the organizers. So - now zoom to today.
Today I am heading down to San Diego for the meeting. And yesterday I found out that there was an editorial in the Wall Street Journal apparently critiquing the plan for having only female speakers. It is entitled "No Men Allowed" by James Freeman. Alas, I do not have access to the editorial as it is behind a paywall. There is also an editorial by Mark Perry at the American Enterprise Institute web site: Can the University of California bar males from presenting research at a biology conference?
So -- clearly, some people do not like the idea of a conference where all the speakers are women. I confess I am still torn about the whole concept for the reasons I mentioned above. However, even though I am torn, I do think it is important to push back against the clear implicit and explicit biases that have occurred against women in relation to speaking at conferences. There is an extensive literature on this topic and on the topic of implicit and explicit biases that may be involved. And I think this conference is an important form of push back. The organizers may in fact get a bunch of grief over not having any male speakers. But they will also provide an important venue for people to get challenged. Conferences with only male speakers occurred for many many years without too many people raising any complaints. And now some still occur but they are generally frowned upon in most places and are becoming rarer at least in my fields. So in a way this conference can serve a similar function as Ruth Bader Ginsburg's dream of an all female US Supreme Court (this analogy was pointed out to me by Karen James). In reference to this concept Ruth Bader Ginsburg said:
"So now the perception is, yes, women are here to stay. And when I'm sometimes asked when will there be enough [women on the supreme court]? And I say when there are nine, people are shocked. But there'd been nine men, and nobody's ever raised a question about that."Of course, gender bias is just one of the forms of bias that happens in STEM fields and with STEM conferences. It is not the only issue we need to worry about or work on. But it is a big one. And the organizers of this meeting have done something bold and risky to confront this issue.
I will report more from the meeting. I would also love to hear what other people think about the plan for this conference.
PS. Thanks to multiple colleagues for some private feedback on this conference. If I get permission I will post details of their comments.
Saturday, February 09, 2019
Symbiosis paper of interest: Host-Microbe Coevolution and Complex Marine Invertebrate Holobionts | mBio
Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts | mBio
O’Brien PA, Webster NS, Miller DJ, Bourne DG. 2019. Host-microbe coevolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio 10:e02241-18. https://doi.org/10.1128/mBio.02241-18.
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
Found out about it on Slack, Twitter and via Google Scholar automated searches so .. caught my attention.
Today's microbial diversity reading: A census-based estimate of Earth's bacterial and archaeal diversity
Louca S, Mazel F, Doebeli M, Parfrey LW (2019) A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 17(2): e3000106. https://doi.org/10.1371/journal.pbio.3000106
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.
The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
Tuesday, January 29, 2019
Wednesday, January 09, 2019
And today in the Twisted Tree of Life Award - the only way to study evolution is to try and make fake reconstructions of past events
Meh - not a fan of this article "Go Ahead, Prove that Eukaryotic Cells Arose— Jonathan Eisen (@phylogenomics) January 10, 2019
Via Endosymbiosis" https://t.co/P3xjoItYhO 1/n
Mind you - the article being discussed sounds nice but the part I don't like is logic here which in essence says "5000 papers in which evolutionary analysis supported endosymbiosis theory are useless" 2/n pic.twitter.com/AaiwqTM1Gx— Jonathan Eisen (@phylogenomics) January 10, 2019
And that the right and only way to do evolutionary inference is by trying to recreate something that happened a billion years ago in an artificial system using yeast - completely and utterly ridiculous actually 3/n— Jonathan Eisen (@phylogenomics) January 10, 2019
This article basically discounts all evolutionary analysis and ends with this inane and totally BS line about this artificial reconstruction "Next to having been there, this is as good as it gets" 4/n— Jonathan Eisen (@phylogenomics) January 10, 2019
This to be is akin to saying "We cannot study history through analysis of archaeology or texts or artifacts but only by creating simulations of historical events in Minecraft or other artificial worlds" 5/n— Jonathan Eisen (@phylogenomics) January 10, 2019
I mean this is remarkably similar to anti-evolution / Intelligent design arguments “If you did not observe it, you can’t prove evolution happened” #aaargh 6/n— Jonathan Eisen (@phylogenomics) January 10, 2019
He even writes “Seeing is believing” - basically discounting all evolutionary inference and following the Intelligent Design logic for critiquing evolution 7/n— Jonathan Eisen (@phylogenomics) January 10, 2019
The more I consider this the more troubled I am by it - basically, he is saying "Any evolutionary study that is not either direct observation, or a recreation attempt, even if that attempt is barely connected to the theory, is not to be believed" 8/n— Jonathan Eisen (@phylogenomics) January 10, 2019