Tattoo World life: Twisted tree of life award

Showing posts with label Twisted tree of life award. Show all posts

Thursday, April 26, 2012

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.

Wednesday, December 7, 2011

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

Monday, September 12, 2011

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 ...

Thursday, August 25, 2011

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

Friday, June 17, 2011

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:

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