Twisted tree of life award – Page 2

Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus

OK, though this is not as bad as printing the wrong form of DNA on the cover Nature has another faux pas. In a recent Nature News story discussing a recent paper on the characterization of venoms in the platypus, Ewen Callaway reports in Poisonous platypuses confirm convergent evolution : Nature News:

By some accounts, being poisoned by a platypus could qualify as punishment in one of Dante’s circles of hell. In one case report2, Australian doctors described their treatment of a 57-year-old man a few hours after he grabbed one of the small marsupials while fishing. The pain was “so bad I started to become incoherent” the man said, and far worse than the shrapnel wounds he took as a soldier. Ibuprofen and morphine provided no relief, and one finger was swollen and ached more than 4 months after the run-in.

The only problem with this is that the platypus is a monotreme, not a marsupial.

From http://kaboodle.nescent.org/?q=node/594

Fortunately Nature does get this correct on the headline for the story “Genome analysis shows that the monotremes and snakes have similar venoms” but the damage is done in the middle.

The mistake in the middle of the article may seem a very minor thing to most of you out there. But @an_dre_a is calling for action on twitter from the monotreme antidefamation league. And I am now posting here and giving Nature my coveted “Twisted Tree of Life Award” (the ninth) to bring attention to this horrendous horrendous offense to monotremes everywhere.

Hat tip to @recher_she on twitter who called my attention to the Nature article because it mentions the “venome” a really #badomics word that I will be writing about later.

Twisted Tree of Life Award #7 #8: Alroy on "Changing the rules of evolution"

Twisted Tree of Life

Every once in a while I give out an award here for bad discussions of evolution in the media or scientific publications. I call this the “Twisted Tree of Life Award.” And here is a doozy. It comes from a recent paper in Science: The Shifting Balance of Diversity Among Major Marine Animal Groups — Alroy 329 (5996): 1191 — Science

The paper is actually pretty interesting. But the last line of the abstract. OMG. It is beyond awful. Here is the full abstract:

The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere’s taxonomic composition by changing the rules of evolution.

That last line saying that the current extinction crisis may change the rules of evolution really really really bugs me. Changing the rules? Please. If they are rules, then, just how, exactly do they change? If they do change, perhaps they should not be rules no?

And as an aside, what is up with Science not printing the full first name of authors? Does that really save space?

Anyway – not much to say here other than that J. Alroy is the winner of my the 8th “Twisted Tree of Life Award” for suggesting that the evidence presented in this Science paper changes the rules of evolution. And a half award goes to the editors of Science for letting this BS get into the abstract.

Previous recipients of this award are

Hat tip to E2 (aka Eric Eisenstadt) for pointing out this article and the strange claim in the last sentence of the abstract.

Twisted Tree of Life Award: NPR on the Evolution of Crying

Well, normally I really like NPR science stories. But this one dug into my anti adaptationism feelings. Adaptationism is, in essence, the practice of saying something must be adaptive (i.e., beneficial), simply because it is there in an organism. Such cases are also referred to as “just so stories” – a play on the old Kipling “Just So Stories“. That is, in essence, people who claim something is adaptive just because it is there are in essence telling you something is this way because it is just so. I am actually not sure of the whole history of using the just-so analogy to refer to adaptationist stories – I know Stephen Jay Gould discussed this a lot in his books and lectures, but not sure who first did it.

Anyway – NPR has an adaptationistic doozy from Morning Edition:

Teary-Eyed Evolution: Crying Serves A Purpose : NPR

Basically, it seems the gist of the argument here is the following line:

Scientists who study evolution say crying probably conferred some benefit and did something to advance our species — because it’s stayed with us.

Wow – that is like straight out of the adaptationist playbook. The problem with this argument is that many things exist and persist in organisms even when they are not adaptive. There are many reasons why this can happen from constraints (e.g., if bones were not adaptive in humans it would be pretty hard to get rid of them) to invisibility to selection (e.g., some features that only show up after reproductive age may not really influence fitness) and so on.

In essence the NPR story is one of the worst examples of adaptationism in the good science press I have seen in a while. Sure this shows up all over the place. But rarely this bad at NPR. The story ends with an even worse line than the rest

Maybe that’s another reason evolution kept humans weeping: Tears help reveal the truth. And that’s because along with the tears, we’ve evolved a very sophisticated ability to interpret them.

Yes that is right. Crying has been maintained in humans because we also evolved another adaptive feature – the ability to interpret tears. So the logic here is that crying is adaptive because it is needed for another adaptive trait for which there is no evidence it is adaptive.

So for their story on crying and for in essence inventing some just so stories to explain why they think it is adaptive, NPR is the recipient of my Twisted Tree of Life Award. Previous recipients are

See also these things for some stuff on evolution of crying:

Darwin in the Crib – oldie but goodie from Carl Zimmer in 2005
Zimmer’s NY Times article related to the above.
A Critique of the Adaptationist Programme from Larry Moran at Sandwalk
My Evolution textbook has some discussion of

Twisted tree of life award #6: Scientific American Origins piece for dissing microbes

There is an interesting series of mini articles in the August 2010 Scientific American tracing the origins of various concepts and things: Origins: Going Back to Where the Story Really Starts: Scientific American

Not open access mind you, but if you have a subscription it is worth checking out. They track the origins of the following:

swiss cheese
paternal child care
computer viruses
animation
sexual reproduction
malaria
fireworks
barbed wire
hand washing in hospitals
human morality
electric cars
the influenza virus
wheeled vehicles
black holes
zero
biodiversity
noodles

Many of the discussions are interesting. Some are a bit trite. But that is not what I am here to report on. I am here to complain about one aspects of the article series: too much emphasis on humans and multicellular organisms as “higher” creatures. There are various subtle phrases here and there that I did not like too much but the parts that really grate on me are the two below:

In the article on biodiversity Melinda Moyer discusses the remarkable possibility that single celled creatures might have in fact had some diversity in them “Today we think of biodiversity in terms of multicellular life, but flowering plants and animals didn’t arrive until relatively recently” she writes. And ends with “It is no comfort to know that the worst catastrophe would still preserve some biodiversity — even if only for the lowly cell.“
In the mini article on sex, Brendan Borrell writes “The truth is, nobody really knows why people — and other animals, plants and fungi — prefer sex to, say, budding.” This of course leaves out all the other eukaryotes that are not plants, animals and fungi that have sex.

And though these are certainly subtle small issues, I feel that Scientific American should do better. So for directly and indirectly dissing the microbes on the planet – I am giving them my coveted Twisted Tree of Life Award #6. Previous winners are listed below:

Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc

Nicholas Wade has a new article in the New York Times critiquing some aspects of the human genome project (A Decade Later, Gene Map Yields Few New Cures – NYTimes.com)

Whether one agrees with his critiques or not, I hope that everyone can recognizes that one section on evolution is, well, awful. Wade writes

First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.

While Mr. Wade may want to believe he and humans in general are somehow “higher” on some evolutionary ladder than other species, I have some news for him

THERE IS NO FU*$ING EVOLUTIONARY LADDER.

Humans are neither higher nor lower than any other organisms. This is an antiquated and inane view of evolution. Sure, humans are smart. Sure we are more complex in some aspects than, say, some bacteria. But new features evolve on ALL branches in the tree of life. And some organisms lose features present in their ancestors. The evolution of complexity is, well complex, sure, but please, “higher” and “lower” organisms? An evolutionary ladder? Uggh.

I do not pay much attention to human GWAS studies, but if Wade’s understanding of them is akin to his understanding of evolution, well, I would then infer that GWAS studies have revolutionized all of medicine. For his butchering of evolution, I am giving Nicholas Wade my 6th coveted “Twisted tree of life award”

—————————-

More on this topic can be found at:
Larry Moran’s Sandwalk
Larry Moran has a good discussion of the genes in the human genome issue (from 2007)
PZ Myers at Pharyngula Chimes in

Twisted Tree of Life Award #4: Hoxful Monsters Blog on "Primitive" Animals

Nothing gets me more riled up in evolutionary writings than the use of the term primitive to describe organisms on a “deep” branch in an evolutionary tree. Thus for the following tree

many people would refer to Species 1 as a primitive organism solely on the basis of this tree. In fact, I just saw this in the Hoxful Monsters blog (see here) where it says:

In April 2008, Cassey dunn et el published their famous phylogenomics work in Nature, which placed Ctenophores at the base of the tree making them most primitive animal on Earth. Before that work Sponges were considered as first animals to branch off from rest of the animals and hence occupied a most basal position in the tree of animals for long time. However, some months later another phylogenomics study carried out by Bernd Schierwater et al ; changed things dramatically by placing Trichoplax as most primitive animal replacing Ctenophores. Now a new phylogenomic study published in online section of Current Biology is making headlines , where Sponges regain their position as most primitive animal on Earth.

This is simply wrong as the term primitive, which I avoid at all costs because it is so frequently misused, should only be used to refer to features of organisms not to the branching pattern in an evolutionary tree. Forget for a minute that “primitive” implies that something else is “advanced”, as if we could determine which is which. And lets pretend instead for a minute that “primitive” could be used in an equivalent manner as “ancestral.” Ancestral is a term used to refer to features of organisms present, as the term implies, in an ancestor. Thus is the organism(s) at the node in the tree labelled with the X had some feature (e.g., lets say, they were green) and Species 4 is green while Species 1 is orange and Species 2 and 3 are purple. In this case, in terms of color, Species 4 has ancestral feature and the other species have derived features. And thus, when I am feeling generous, I will grant that one could sort of use the term primitive to say “Species 4 is primitive in terms of color.” I don’t like this usage, because primitive implies something about quality that ancestral and derived do not. But it is not so horribly wrong that I cringe.

But I would like to make two more points in terms of the way primitive is misused.

First, even if one species had a large number of ancestral features (and thus for those features resembled an ancestral organism), that species certainly will have some derived features as well. Thus ancestral, derived, and primitive (ick) should only be used to refer to features, not organisms.
Second, the particular position a species occupies in a tree does not tell use whether it has ancestral or derived features. Thus is my color example above, Species 1 does not have the ancestral phenotype — it has a derived one. Thus calling organisms that branch deeply in a tree “primitive” is wrong not only because it is referring to an organism not a feature but also because deep branching does not imply ancestral features.

In other words, the fact that if you look only at species in the tree, that Species 1 is the deepest branching individual species, does not in any way tell whether Species 1 has primitive (i.e., ancestral) features. Features present in the common ancestor of the entire group (i.e., the organisms at node X) are the ancestral features. These features could change on any of the branches leading to Species 1,2,3, and 4. If they change, then the descendants will have derived features. If they stay the same they will have ancestral features. The branching order of the species does not explicitly tell us which one retains ancestral features.

This inaccurate use of phylogenetic trees to imply primitive features drives me batty. I was disappointed to see this phylogenetic gobbledygook being used in the HoxFul Monsters blog. And thus, Hoxful Monsters is the winner of my fourth “Twisted Tree of Life” award.

Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria

Was browsing Twitter and I saw one post that caught my eye. @MicrobeWorld, which by the way, rocks, wrote

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water http://bitly.com/15l9mR

This caught my eye because, well, I study radiation resistance some of the time and the “old as dirt” statement seemed weird.

The article being referred to was in the Columbus Dispatch (The Columbus Dispatch : Tricking toxins) and it was about some interesting work on Shewanella by Brian Lower and others from Ohio State. The work involves using one particular species of Shewanella for bioremediation of radiative waste. The problem however is in the lead in to the article. This is painful to me. It says

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water.

Shewanella oneidensis bacteria have existed for billions of years, thriving even when the Earth’s atmosphere lacked oxygen.

This is just so so so wrong. Shewanella oneidensis is one species of a large group in the genus Shewanella which itself is part of one subgroup (the gamma group) of the Phylum Proteobacteria (I note I helped analyze the genome sequence of this species a few years ago – see paper here). While it is possible (though not certain) that the Phylum Proteobacteria was established billions of years ago, it is certain that Shewanella oneidensis did not exist at that time. Perhaps this species has been around for tens of millions of years but certainly not billions. This would be like saying “Humans have been around for hundreds of millions of years” simply because animals have been around for that long. In the context of humans the statement is clearly absurd. It is in fact equally absurd in the context of bacteria. And for this, the Columbus Dispatch is getting my third Twisted Tree of Life Award.

Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms

Well, I love Science Friday. I listen to podcasts of it now almost every day when I bike to work. It is a brilliant show, covering a wide range of science and science related topics in depth. Plus it is freely downloadable in a variety of formats. And they have a great website too. But every once in a while they get something a bit wrong. Yesterday, on my way home from a new introductory biology class we are teaching at Davis on “The Tree of Life” (which I will write more about later), I was listening to a Science Friday about Fungi (Science Friday Archives: The Fabulous Fungi). And unfortunately, in the introduction, Joe Palca started off with a pretty outdated discussion of the tree of life.

When you ask people to name the kingdoms, most people get the big ones, animals, plants, bacteria. Some people may even come up with the protists. But there is one more. Here’s a hint. Yeast are part of it. So are shitakes. Are you getting it? Well the answer is fungi.

Yes, they are in fact referring to the Whittaker “Five Kingdoms” tree of life, which is no longer in use. (I am placing an image here from my Evolution Textbook) where we talk in Chapter 5 about the history of various trees of life that have been used. The figures from our book are available for free at the book site)

Today we talk about the Three Domains (Bacteria, Archaea and Eukaryotes) and within each of those domains, they are many lineages (which are sometimes referred to as kingdoms). But the five kingdom concept is done and gone. The modern tree looks more like the following (which is an adaptation for our book of a tree by Baldauf).

Mind you, the show on Fungi is worth listening to (although they did miss the opportunity to use the tree of life to answer a question that came up on “Are fungi from outer space?” – the answer should have been – “No, fungi are deeply embedded within the tree of life on this planet, so if life came from elsewhere, it was at the beginning of the origin of life”).

Unfortunately, I could not call in to the show (as I have done before) to try and comment on these issues (since I was not listening live). So instead, I am giving Science Friday my Second “Twisted Tree of Life” Award for ignoring the new concepts of the tree of life that have been in play since Woese, Fox and others first laid the groundwork for the existence of the Archaea.