Twisted tree of life award – Jonathan Eisen's Lab

Twisted tree of life award: throwback PR from an ingrained Oregon State

Just got pointed to this PR: Unwanted impact of antibiotics broader, more complex than previously known — ScienceDaily

It has one of the worst microbe-evolution sections of text I have seen in a long long time:

Mitochondria plays a major role in cell signaling, growth and energy production, and for good health they need to function properly.

But the relationship of antibiotics to mitochondria may go back a long way. In evolution, mitochondria descended from bacteria, which were some of the earliest life forms, and different bacteria competed with each other for survival. That an antibiotic would still selectively attack the portion of a cell that most closely resembles bacteria may be a throwback to that ingrained sense of competition and the very evolution of life.

Yup. That antibiotics that target bacteria also affect mitochondria is a throwback to that ingrained sense of competition and the very evolution of life.

Can anyone – anyone – please – please – tell me what that means?

For this, I am giving the folks from Oregon State a coveted Twisted Tree of Life Award.

Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium

Well, this is one of the bigger screw ups in terms of evolution I have seen at a major journal in a while. See the following paper in Nature: The catalytic mechanism for aerobic formation of methane by bacteria : Nature. The paper discusses some functions of “the ocean-dwelling bacterium Nitrosopumilus maritimus.” Some of what is reported in the paper is perhaps interesting (alas I do not have access). But painfully, there is one big big big big mistake – you see Nitrosopumilus maritimus is not a bacterium. It is an archaeon (see for example this paper on its genome).

I got pointed to this by Uri Gophna (in an email and in a comment on my blog)(all see this on Twitter) Sure – some people debate the structure of the tree of life. But I am pretty certain the authors here (Siddhesh S. Kamat, Howard J. Williams, Lawrence J. Dangott, Mrinmoy Chakrabarti & Frank M. Raushel) are not trying to make a statement about monophyly of bacteria or just what archaea are. They just made what seems to be a colossal screw up. And Nature not only let them, but added to it with things like their “Editors Summary”:

Novel bacterial biosynthesis of methane
Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S-adenosyl-L-methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate.

And for this taxonomic alchemy (converting an archaeon to a bacterium) I am awarding them and Nature my coveted “Twisted Tree of Life Award #16″.

UPDATE 5/28 7AM

I love the ad that came up while I was writing this post and searching for some information. I think Nature could use the services from this ad:

Twisted tree of life award #15: NBC News on "Junk DNA mystery"

Oh for fu$*# sake. Really MSNBC? I mean, I know perhaps I should not expect much from some in the press but this is just awful: ‘Junk’ DNA mystery solved: It’s not needed.

Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage). This article has some complete and utter crap:

Some parts that I have issues with:

The headline: “‘Junk’ DNA mystery solved: It’s not needed.” The headline is silly but alas it is consistent with what is in the article.
“So-called junk DNA, the vast majority of the genome that doesn’t code for proteins“. So – they have redefined junk DNA as all non coding DNA?
“For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn’t seem to contain genes or turn genes on or off.” Apparently there is an entity out there known as “The Genome”.

And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.

“At least for a plant, junk DNA really is just junk — it’s not required.” Except that they did not show this – they just showed that one plant can have a small genome and not have a lot of “junk” as they call it, which of course does not really say anything about what “junk” does or does not do in other organisms.
“Nobody’s really known what junk DNA does or doesn’t do” apparently calling into question the some 10,000 plus papers on the topic.

Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes. Oh and the organism is complex. Therefore, apparently, it follows that

“The findings suggest junk DNA really isn’t needed for healthy plants — and that may also hold for other organisms, such as humans.”

And this leads us to ‘Junk’ DNA mystery solved: It’s not needed.

So – basically – if ONE FUCKING ORGANISM DELETES SOME OF IT’S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

Aaaaaaaaaaaaaaaaaaargh.

And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.

Past winners:

UPDATE 5/17/13

Some other discussions of this paper and related to my critique (though not always agreeing with me)

Knight School of Journalism: A Weird Little Plant is Nearly Free of Junk DNA. Big Contentions Underlie Seemingly Cute Story
From T. Ryan Gregory Genome reduction in bladderworts vs. leg loss in snakes …
Deconstructing Nature’s “plant without junk DNA” story | Genetic …
From Dan Graur: The Logical Fallacy of Jonathan Eisen ‏(a.k.a. @phylogenomics) and the Theological Implications of the Bladderwort Genome

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.

Twisted tree of Life Award #13: Press release from U. Oslo on new protozoan

Wow. Just got pointed to this press release Rare protozoan from sludge in Norwegian lake does not fit on main branches of tree of life (hat tip to Bill Hooker). It is a long PR. And it is riddled with many examples of evolutionary mumbo jumbo – each of which on their own could win a Twisted Tree of Life Award here. And together, well, I am just going to give it one award – the Twisted Tree of Life Award #14.

Here are some statements that are, well, dubious, and/or painful.

Biologists all over the world have been eagerly awaiting the results of the genetic analysis of one of the world’s smallest known species, hereafter called the protozoan, from a little lake 30 kilometer south of Oslo in Norway.

Wow – really? All over the world?
And why not tell us what the F#&$# it is? Where is the name of the organism? WTF?

When researchers from the University of Oslo, Norway compared its genes with all other known species in the world, they saw that the protozoan did not fit on any of the main branches of the tree of life. The protozoan is not a fungus, alga, parasite, plant or animal.

That is right. There are five main branches on the tree of life. Fungi. Alga. Parasites. Plants. And animals. Uggh.

His research group studies tiny organisms hoping to find answers to large, biological questions within ecology and evolutionary biology, and works across such different fields as biology, genetics, bioinformatics, molecular biology and statistics

Yes, and I study tiny organisms to answer small questions.

Life on Earth can be divided up into two main groups of species, prokaryotes and eukaryotes. The prokaryote species, such as bacteria, are the simplest form of living organisms on Earth.

Yup, two main groups. As of 40 f3$*@# years ago.

The micro-organism is among the oldest, currently living eukaryote organisms we know of. It evolved around one billion years ago, plus or minus a few hundred million years.

OMG. This is a MODERN ORGANISM. It did not evolve a billion years ago. It is no older than ANYTHING ELSE ON THE PLANET. AAAAAARRRGH.

The tree of life can be divided into organisms with one or two flagella

What?
The tree of life can also be divided into organisms with one or two penises.

Just like all other mammals, human sperm cells have only one flagellum. Therefore, humankind belongs to the same single flagellum group as fungi and amoebae.

I don’t even know what to say here.

The protozoan from Ås has four flagella. The family it belongs to is somewhere between excavates, the oldest group with two flagella, and some amoebae, which is the oldest group with only one flagellum.

Wow – no prior description of the major groups of eukaryotes and now we use excavates (kind of technical) and amoebae (not technical). Translation error?
But even w/ translation issues still very strange.

Were we to reconstruct the oldest, eukaryote cell in the world, we believe it would resemble our species. To calculate how much our species has changed since primordial times, we have to compare its genes with its nearest relatives, amoebae and excavates,” says Shalchian-Tabrizi.

What? Their species has been around since primordial times? What? That is one really old cell.

The protozoan lives off algae, but the researchers still do not know what eats the protozoan.

Why does something have to eat it?

The protozoan was discovered as early as 1865, but it is only now that, thanks to very advanced genetic analyses, researchers understand how important the species is to the history of life on Earth

Very advanced? Like, what? Sequencing?

The problem is that DNA sequences change a lot over time. Parts of the DNA may have been wiped away during the passing of the years. Since the protozoan is a very old species, an extra large amount of gene information is required

What? Since it is old they need more DNA? What?

I could go on and on. I won’t. But I will say one last thing that drives me crazy. There is no paper attached to the press release in any way I can tell. So all we are left with is this very very very very bad PR. Ugh.

Draft post cleanup #13: Twisted tree of life award: MSNBC, Aliens and Photosynthesis

Yet another post in my “draft blog post cleanup” series. Here is #13 from July 2010.

I wanted to give this article a “Twisted Tree of Life Award“:

How to find aliens: Follow the photosynthesis – Technology & science – Space – Space.com – msnbc.com

It is pretty painful to me. Basically the people they are quoting argue that since “complex” life on Earth requires oxygen and since oxygen only comes from photosynthesis, therefore we should look for planets where photosynthesis is possible as the place where life is most likely to be interesting. Uggh. So many things in the article I did not like … but just not enough time I guess to bitch about it then. I will leave it to readers to decide for themselves I guess …

Twisted Tree of Life Award #12: Billion Year Old Smart Bacteria That Perfectly Treat Cancer

OMG – for crying out loud. In the following story Billion-year-old Bacteria Could be Medical Goldmine Fox News discusses studies of marine cyanobacteria at the University of Florida. It is so wrong in so many ways I do not know where to begin. Watch the video first for layers of trouble. Then, if you dare, read the article. Among the painful parts:

All cyanobacteria are basically lumped together into a single entity

Cyanobacteria are the oldest organisms on earth – billions of years old – which means they must have have evolved amazing chemistry to deter predators. Wow – by the same logic – bacteria in general should be even better – because bacteria are even older than cyanobacteria. And therefore – if one focused on ALL bacteria, we should find even better predator deterring chemicals. Wait – actually – why not target all life. Surely, if cyanobacteria have perfected the art of deterring predators by the fact that they are billions of years old surely the existence of life is proof that there must be some protection against predators and therefore “living organisms” have the best deterrence systems.

Then they make the leap from cyanobacteria surviving for billions of years by deterring predators to – wait for it – wait – hold on – be patient – wait for it – to – yes that is right – deterring “a devastating human predator – cancer.” At least they did not reveal that cancer is also billions of years old.

And then, without any further detail, they leap from this insight to that apparently the researchers have found that the cyanobacteria make the nearly perfect anticancer drug that “has a 1-2 punch” to inhibit growth factors and receptors to be extremely potent.

Furthermore they tell us that these cyanobacteria “are valuable because unlike similar species they are smart – targeting bad cells and sparing healthy ones.” That is right, the cyanobacteria have been smart enough to target their drugs to human cancer cells – something they must encounter frequently in their marine life.

Oh for f3#*$# sake. I can’t even write about this anymore.

I will just give out a well deserved “Twisted Tree of Life” award here. Not sure though who should get it – because it is unclear if this material came from U. Florida or if the station somehow came to it itself.

Past winners include

No award to give out but here are some lessons in using Google’s image search to find an image source

Was going to blog about the distorted tree of life that BMC Biology used for an ad in the Scientist (note – I am a big fan of both BMC Biology and the Scientist, but the ad still irked me). But I was not really sure where the image came from since the ad does not say much of anything about the source. So I used a new trick I learned last week. I scanned the ad:

As all of you should be able to see, this tree does not do such a good job with microbial diversity. And as an official Guardian of Microbial Diversity, I was offended. So the question now was – from where exactly did this tree come? And could I find BMC Biology saying something important about the figure so that then I could snark about them in my blog and give them a Twisted Tree of Life Award.

Last week in response to an email from some folks at ASM about tracking down the source of an image, I discovered a cool new trick which I used here. I went to Google’s image search page:

And instead of typing anything in, I clicked on the little camera icon inside the search box

And that gave me a new window:

And I uploaded the scanded ad and presto, this window came up:

With all sorts of pages with similar images. Pretty cool. And after browsing a few of them I found that the page on BMC Biol. fridge magnets which they give away at conferences. And for the one with the offending tree they say

The problem of representing all of biology is encapsulated in the image we have devised as an emblem for the fusion of BMC Biology and Journal of Biology. Our protocellular lipid bilayer surrounding a circular representation of a rootless phylogenetic tree omits explicit reference to much that is fundamental, critical and topical in biology, and outrageously distorts the phylogenetic tree. You will have to love the image for itself.

Well well well. Kind of awkward to give someone an award for bad evolution mojo when they know full well that their evolution mojo is bad. So alas, no Twisted Tree of Life Award for BMC Biology. Kudos to them for knowing / acknowledging that the tree might have some issues. Now what I really want is to get me one of them magnets. Issues aside, the tree is pretty …

UPDATE 9/3/2012
BMC Biology has an editorial about this here: What is wrong with this picture?

Twisted tree of life award #11: National Geographic for emphasizing Five Kingdoms & no Bacteria/Archaea

Well, I really don’t want to complain so much but I guess I am on a roll recently. And an email from Will Trimble pointed me to a news story that I cannot resist dissing a little bit. The story is from National Geographic (86 Percent of Earth’s Species Still Unknown?) and discusses the recent paper on number of species on Earth that I critiqued a bit in my last blog post: Bacteria & archaea don’t get no respect from interesting but flawed #PLoSBio paper on # of species on the planet

The National Geographic article alas does not discuss the problems with the paper in terms of microbes (though Carl Zimmer’s NY Times article How Many Species on Earth? It’s Tricky does as does a Google Plus post from Ed Yong. But that is not what I am here to moan about. I am here to give out an award – a Twisted Tree of Life Award. You see, I give this out when people who should generally know better do something bad relating to evolution. And National Geographic (or, well, Traci Watson, the author) did in this article. The complaint I have is the emphasis on the Five Kingdoms. She writes.

Scientists lump similar species together into a broader grouping called a genus, similar genera into a still broader category called a family, and so on, all the way up to a supercategory called a kingdom….. There are five kingdoms: animals, plants, fungi, chromists—including one-celled plants such as diatoms—and protozoa, or one-celled organisms.

First of all, except for some of the most old school of old school folks, biology has moved way way beyond the five kingdoms. In fact, I gave out an award to Science Friday in 2008 for emphasizing the five kingdoms: The Tree of Life: Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms. But I guess the author/editors did not see that. Basically what I said there was that the modern view is much more complex than the five kingdoms with things like “Domains” (i.e., bacteria, archaea and eukaryotes) as the three main lineages of life. And within eukaryotes there are many more subgroups than the ones the five kingdoms system recognized.

Perhaps even weirder though, the five kingdoms they list in the National Geographic article are not the same five kingdoms from Whittaker in 1969 which is the traditional source of the five kingdom system. Whittaker had Monera (i.e., organisms without nuclei aka prokaryotes), Protists (single celled eukaryotes not in the other groups), Plants, Fungi and Animals.

Not quite sure where they came up with the five listed in the National Geographic article. Most likely from Cavalier-Smith who has been pushing the Chromists.

Figure 1. From Biol Lett. 2010 June 23; 6(3): 342–345.

But not sure what happened to the Monera. Or, another way of putting this is that they appear to think that bacteria and archaea are not organisms.

So even if you still follow the sort-of five kingdom system, or Cavalier-Smith’s six kingdom system – the National Geographic five kingdoms leave out all bacteria and archaea. And I would say most if evolutionary biologists these days do not use either the five kingdom or six kingdom system and instead use something much more elaborate, with many more eukaryotic groups and multiple groups of non-eukaryotes.

So – for leaving out bacteria and archaea entirely and for pushing the 5/6 kingdom system that seems, well, out of date, I am giving National Geographic and Traci Watson my coveted Twisted Tree of Life Award.

Previous winners include

Twisted tree of life award: @Discovermag for article on Lynne Margulis

Well, if you can, for a minute, ignore that fact that in Discover Interview: Lynn Margulis Says She’s Not Controversial, She’s Right | Evolution | DISCOVER Magazine Discover Magazine in essence is promoting some of the refuted ideas Lynne Margulis has about HIV. Sure they hint in part that they think she is over the top but they also give her a soapbox to spout some of her latest absurdities on HIV and such. I would suggest you don’t even read the main part of the Discover article. Just read Tara Smith’s discussion of it: Margulis does it again : Aetiology. Margulis should not be given such prominence in a magazine like Discover. But that is not what I am hear to write about. I am hear to point out that Discover also sets up a red herring for Margulis. In the beginning of the article, it is written:

“A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else.”

Seriously? Scientists today do not recognize five groups. Scientists today have moved past that to recognize and/or argue about bacteria, archaea and eukaryotes – the three domains of life. These three groups were first proposed in 1977 by Carl Woese and colleagues. Did Discover somehow miss the last 34 years of science? WTF? For setting up such an evolutionary red herring in this painful interview with Lynne Margulis, I am giving Discover Mag my coveted “Twisted tree of life award“. Past winners are: