Another good science story.

I have been a bit harsh with science writers on a few occasions, though this has often been in good fun. I actually have a lot of respect for (good) science writers, and I think their job is a very important one — which is why I think it is critical that they do it well. If they were irrelevant, they would garner no attention from scientist-commentators like me.

A few times, I have pointed out stories that I think are very good, and have given credit where it is due. I single out JR Minkel, Aria Pearson, Heather Kowalski, and of course Carl Zimmer as excellent examples.

I will continue to point out both good and bad science writing, and to contribute where I am needed in the form of interviews or commentary. Today I want to link to another good story, this time a press release from the University of Bristol as posted by ScienceDaily.

How The Discovery Of Geologic Time Changed Our View Of The World

This piece does the opposite of my guide to writing a bad science story. It provides some historical context. It shows how knowledge has accrued through the efforts of many researchers. It highlights the difficulty of getting a new idea recognized and how even “revolutionary” propositions do not become accepted overnight. Plus, it’s always useful to know some history of science and to give credit to those giants upon whose shoulders we stand.


What’s wrong with this figure?

There is a story on Science News Online entitled “Genome 2.0“. The author has certainly done a lot of legwork and has tried to present a detailed discussion of a complex topic, and for that he deserves considerable credit. (He clearly hasn’t taken my guide to heart). That said, it is unfortunate that the author has fallen into the trap of repeating the usual claims about the history (everyone thought it was merely irrelevant garbage) and potential function (some is conserved and lots is transcribed, so it all must be serving a role) for “junk DNA”. As a result, I won’t comment much more on it. One thing that may be relevant to point out about this story in particular is the first figure it uses. This is a figure I have seen in a few places, including in the scientific literature. It makes me cringe every time because it reveals a real problem with how some people approach the issue of non-coding DNA. And so, 10 points to the first person who can point out what is deeply problematic about the interpretation it is often granted. I include the legend as provided in the original report.

JUNK BOOM. Simpler organisms such as bacteria (blue) have a smaller percentage of DNA that doesn’t code for proteins than more-complex organisms such as fungi (grey), plants (green), animals (purple), and people (orange).


(See also Genome size and gene number)
________________


Update:

The 10 points has been awarded twice on the basis of two major problems being pointed out.

The first is that the graph arranges species according to % noncoding DNA and assumes that everyone will agree that the X-axis proceeds from less to more complex. This is classic “great chain of being” thinking. No criteria are specified by which the bacteria are ranked (and it is simply ignored that Rickettsia has a lot of pseudogenes which appear to be non-functional), which is bad enough. Worse yet, there is really no justification for ranking C. elegans as more complex than A. thaliana other than the animal-centric assumption that all animals must be more sophisticated than all plants.

The second, and the one I had in mind, is that this is an extremely biased dataset. Specifically, it is based on a set of species whose genomes have been sequenced. These target species were chosen in large part because they have very small genomes with minimal non-coding DNA. The one exception is humans, which was chosen because we’re humans. As has been pointed out, even if you chose a few of the more recently sequenced genomes (say, pufferfish at 400Mb and mosquito at 1,400Mb) this pattern would start to disintegrate. If you look at the actual ranges or means of genome size among different groups, you will see that there are no clear links between complexity and DNA content, despite what some authors (who focus only on sequenced genomes) continue to argue.

To illustrate this point, this figure shows the means (dots) and ranges in genome size for the various groups of organisms for which data are available. This represents estimates for more than 10,000 species. This is intentionally arranged along the same kind of axis of intuitive notions of complexity just to show how discordant “complexity” and genome size actually are. Humans, it will be noted, are average in genome size for mammals and not particularly special in the larger eukaryote picture.

Means and ranges of haploid DNA content (C-value) among different groups of organisms. Click for larger image. Source: Gregory, TR (2005). Nature Reviews Genetics 6: 699-708.

Maybe you will join me in cringing the next time you see a figure like the one in the story above.

Update (again):

Others have criticized this kind of figure before. As a case in point, see John Mattick’s (2004) article in Nature Reviews Genetics and the critical commentary by Anthony Poole (and Mattick’s reply). Obviously, I am with Poole on this one.

Anatomy of a bad science story.

There are many good science writers and press officers around. This post is not for them, as they will certainly reject all of its key points. Nor is it for the members of the media who are already adept at producing sensationalistic, inaccurate, or downright ridiculous science news stories. This post is for those writers somewhere in the middle who sometimes get it wrong but can’t quite master the art of atrocious science reporting.

Here, then, is a concise guide for how to write really bad science stories.

1. Choose your subject matter to be as amenable to sensationalism as possible.

Some scientific studies may be considered elegant and important by scientists, but if they help to confirm previous thinking or provide only incremental advances in understanding, they are not newsworthy. What you need is something that will generate an emotional rather than intellectual response in the reader.

(If you’re stuck on this step, try coming up with a topic that fits into Science After Sunclipse‘s handy list of categories for science stories.)

2. Use a catchy headline, especially if it will undermine the story’s credibility.

The headline is what draws the reader in, and it is very important that this be as catchy and misleading as possible. Try to focus on outrageous claims. “Such-and-such theory overthrown by this-and-that discovery” is a good template. If possible, have an editor who has not read the story or knows very little about the topic come up with a headline for you.

3. Overstate the significance and novelty of the work.

Do your best to overstate the importance of the new discovery being reported. This is especially relevant if you are writing a press release at a university or other large research institution. The discovery must, at the very least, be described as “surprising”, but “revolutionary” is vastly more effective. Indeed, the reader should wonder what, if anything, those idiot scientists were doing before this new research was conducted (see step 4). Avoid implying that there is a larger research program underway in the field or that the new discovery fits well with ideas that may be decades old. Also, if the discovery — no matter what it is — can be linked, however tenuously, to curing some human ailment, so much the better.

(For writers reporting about genomics: if your story is outrageous enough, you may be eligible for an Overselling Genomics Award; note, however, that competition for this distinction is intense).

4. Distort the history of the field and oversimplify the views of scientists.

Whenever possible, characterize the history of the field in which the discovery took place as simplistic and linear. It is very important that previous opinion in the field be seen as both monotonic and opposed to the new discovery. If there are signs that researchers have held a diversity of views, some of which are fully in line with the new finding, this will undermine your attempt to oversell the significance of the study (see step 3). For this, there are few better examples than recent work on so-called “junk DNA“. Here, authors of news stories have managed to convince readers that “junk” was unilaterally assumed to mean biologically irrelevant, and that it is only in the face of new discoveries that stubborn scientists are being pushed to reconsider their opinions. The fact that both of these are utter nonsense shows how effective this approach can be.

5. Remember that controversy sells, and everyone loves an underdog.

If the results of a new study do not contradict some long-held assumption or incite disagreement among scientists, then readers will have little interest. As a consequence, it is important to characterize science as a process of continual revolutions (see steps 3 and 4) rather than one of continuous improvement of understanding. Refinement and expansion of existing ideas should not be implied. If there is no real controversy, invent one. And, whenever possible, set it up as a “David vs. Goliath” conflict between an intrepid scientist and the stuffy establishment.

6. Use buzzwords and clichés whenever possible.

It doesn’t matter if the words are used inappropriately or appeal to common misconceptions (see step 7), if it is catchy or well known, use it and use it often. This is particularly important if you would otherwise have to introduce readers to accurate terminology and novel concepts. “Genome sequencing” should be dubbed “cracking the code” or “decoding the blueprint” or “mapping the genome”, for example, even though these clichés are quite inaccurate.

7. Appeal to common misconceptions, and substitute your own opinions and misunderstandings for the views of the scientific community.

It is important that readers’ misconceptions not be challenged when reading a news story. In fact, the more a report can reinforce misunderstandings of basic scientific principles, the better. This can be combined with step 6 to good effect. It is also helpful to insert your own views and misunderstandings as though they were those of the scientific community at large. For example, if you find something confusing, mysterious, or (un)desirable, assume that the scientific community as a whole shares your view.

8. Seek balance, particularly where none is warranted.

A primary tenet of journalism is that it present a balanced view of the story and not make any subjective judgments. The fact that the scientific community has semi-objective methods for determining the reliability of claims (such as peer review and the requirement of repeatably demonstrable evidence) should not impinge on this. It is therefore important to present “both sides” of every story, even if one side lacks any empirical support and is populated only by a tiny minority of scientists (or better yet, denialists and cranks). This does not necessary conflict with step 5, because a false controversy can be set up using an appeal to balance. For example, a productive strategy is to provide one quote from someone at the periphery of the field and one quote from a recognized expert to make it seem as though there is debate about an issue within the scientific community. Under no cricumstances should you explain why the scientific community does not accept the views of the non-expert. This has proven very effective in stories about issues that are controversial for political but not scientific reasons, such as evolution and climate change.

9. Obscure the methods and conclusions of the study as much as possible.

Try not to give many details about the study. A simplistic analogy is much better than actually describing the methodology. Better yet, don’t discuss the methods at all and simply focus on your own interpretation of the conclusions. Be sure to describe said conclusions in terms of absolutes, rather than the probabilistic or pluralistic ways in which scientists tend to summarize their own results. Error bars are not news.

10. Don’t provide any links to the original paper.

If possible, avoid providing any easy way for readers (in particular, scientists) to access the original peer-reviewed article on which your story is based. Some techniques to delay reading of the primary paper are to not provide the title or to have your press release come out months before the article is set to appear. An excellent example, which also combines many of the points above, is available here.

This list is not complete, but it should suffice as a rough guide to writing truly awful science news stories.


The press going ape again.

Here’s a headline from the AFP in Paris (via Yahoo News):

Fossil find pushes human-ape split back millions of years

This is a heck of a lot better than some of the truly nonsensical proclamations of the press about the discovery some important fossils, namely eight molars and a canine tooth from a (presumed) ancestor of gorillas, e.g. New Fossil Ape May Shatter Human Evolution Theory. But I still have some problems with this story.

I’m no anthropologist, and I do not generally follow the specialized literature of that field closely. But as far as I know, it is now very well established that humans and chimpanzees are more closely related to each other than either is to gorillas. That is what the molecular data indicate, in any case. Here’s a representation of the relationships among our closest living relatives:

This means several things. First, that there is no natural category called “apes” that does not include humans. Humans are apes. Second, that there was no single split between the ancestors of “apes” and those of humans. Different lineages split at different times. The split between the ancestor of orangutans and the ancestor of the other apes (gorillas + chimps + humans) probably occurred first, then the split between the ancestor of gorillas and that of the remaining apes (humans + chimps), and then the split between the ancestor of chimps and humans. (And then splits between the ancestor of chimps and bonobos and various now-extinct relatives thereof, and between the ancestors of various hominins).

(Just in case it doesn’t go without saying, humans are not descended from chimps, they share a common ancestor with chimps. Chimps are cousins, not grandparents, to humans. Further, it is just as accurate to say that “orangutan ancestors diverged from the ‘human’ lineage” as it is to say that “human ancestors diverged from the ‘orangutan’ lineage”. There is no main trunk from which offshoots diverge, there are just branchings within a bush.)

In this particular news story, the reporter notes that “the new fossils, dubbed ‘Chororapithecus abyssinicus‘ by the team of Japanese and Ethiopian paleoanthropologists who found them, place the early ancestors of the modern day gorilla 10 to 10.5 million years in the past, suggesting that the human-ape split occurred before that.”

Moving the split of the ancestors of gorillas from the ancestor of chimps + humans back does not affect the “human-ape split”. Why? Because there was no such split. Move the gorilla lineage divergence back from 6-8 to 10-10.5 million years (My), that’s fine, but it does not automatically tell you when the human and chimpanzee ancestors’ lineages split, because that occurred later (nonetheless, the authors of the original paper suggest a new divergence for chimp/human ancestors at 9 My). In contrast, if you found an older split for the ancestors of humans and chimpanzees, you might have to move some splits that happened before it back also. As a result, there are arguments that pushing the gorilla lineage split back to 10 My from the current 6-8 My would require moving the orangutan lineage split way back (the authors of the original article say to 20 My).

Notably, the author of the news story also reports that “Conventional scientific wisdom, based on genetic “distances” measured by molecular geneticists, had placed the divergence between chimps and humans some five to six million years ago. Orangutans are thought to have parted company with our ancestors 13 to 14 million years ago.” As a very general proposition, and not including any nuanced discussion, gorillas would be expected to have ancestors of an age somewhere in between 5-6 and 13-14 million years, and 10-10.5 My is right in between these.

Maybe I am missing something, but as interesting and important as this discovery is for understanding some specifics of gorilla evolution, it does not shake things up that much as far as the other apes, including a certain hairless one, are concerned. That is, if these really are teeth from a direct ancestor of gorillas and not an example of convergence according to diet in a non-ancestral species, as some people have already suggested it might be. The question of why the molecular data and the fossils don’t quite agree is interesting, but that’s a pretty standard issue.

Finally, let me say once again that this sort of case is a question about the path of evolution, the specific branchings and timings thereof in the history of particular lineages, and has no bearing on the fact of evolution, namely whether or not species are related through common ancestry and descent with modification. Find me a gorilla fossil older than 500 My and we’ll talk about substantial challenges to the fact of evolutionary relationships.

———-

The original report and comments article in Nature are:

Suwa, G., Kono, R.T., Katoh, S., Asfaw, B., and Beyene, Y. 2007. A new species of great ape from the late Miocene epoch in Ethiopia. Nature 448: 921-924.

Dalton, R. 2007. Oldest gorilla ages our joint ancestor. Nature 448: 844-845.


T. rex could outrun humans?

Is it just me, or is there a major difference between

T. Rex Could Outrun Humans

(which is what LiveScience proclaimed)

and

T. rex Could Have Outrun Humans”

?

No, I am not talking about the annoying, inaccurate notation of the species name, but the (probably unintentional) invocation of an image of T. rex coexisting with and outpacing H. sapiens.

The story itself correctly says that T. rex is thought to have been able to reach speeds higher than humans. Incidentally, this is the same author who posted a previous story about which I recently complained.

Maybe I am just getting too nitpicky at this point.


A surprisingly silly interview.

LiveScience is continuing with their series on nature’s “Greatest Mysteries”. Today it’s “What drives evolution?“.

In the second paragraph, we find this intriguing question:

Natural selection is accepted by scientists as the main engine driving the array of organisms and their complex features. But is evolution via natural selection the only explanation for complex organisms?

No, it isn’t. Genetic drift also plays a major role. However, as Dawkins points out repeatedly, natural selection is the only known mechanism capable of resulting in complex adaptations. The legitimate debate is therefore about how much phenotypic (or genetic) change is adaptive and how much is a product of chance. I wouldn’t consider it a “great mystery” but a debate about the relative contributions of fairly well understood mechanisms. Dawkins sees adaptations as the only interesting things to explain. Lynch (2007) provides an equivalently extreme argument from the drift side of the aisle. But this can’t be what the author has in mind, as it is all very standard.

“I think one of the greatest mysteries in biology at the moment is whether natural selection is the only process capable of generating organismal complexity,” said Massimo Pigliucci of the Department of Ecology and Evolution at Stony Brook University in New York “or whether there are other properties of matter that also come into play. I suspect the latter will turn out to be true.”

So we see that, indeed, the discussion is not about whether processes besides selection can generate complexity (they can, though it may not be adaptive complexity). It’s about whether totally different processes are at play. Reading Pigliucci’s statement immediately brings to mind thoughts about self-organizing complexity as emphasized by Stuart Kaufman and others about 15 years ago. Interesting ideas, but they didn’t really lead anywhere. But this is not what is discussed, and it’s here that the story takes a turn for the bizarre.

“Over the past decade or two, scientists have begun to suspect that there are other properties of complex systems (such as living organisms) that may help, together with natural selection, explain how things such as eyes, bacterial flagella, wings and turtle shells evolve,” Pigliucci told LiveScience.

One idea is that organisms are equipped with the flexibility to change their physical or other features during development to accommodate environmental changes, a phenomenon called phenotypic plasticity.

Phenotypic plasticity is a “property of matter”?

The change typically doesn’t show up in the genes. For instance, in social bees, both the workers and guards have the same genomes but different genes get activated to give them distinct behaviors and appearances. Environmental factors, such as temperature and embryonic diet, prompt genetic activity that ends up casting one bee a worker and the other a guard.

The cells in my fingers typing these words are very different from the cells in my brain thinking them, but they contain the same genome. The exact details of gene regulation and cell differentiation are still being studied, but this hardly constitutes either a “great mystery” of evolution or a challenge to Darwinian mechanisms. Same goes for castes within a bee hive, which has been described as being like a superorganism.

And just to prove that this is all very standard:

If beneficial, this flexibility could be passed on to offspring and so can lead to the evolution of new features in a species. “This plasticity is heritable, and natural selection can favor different kinds of plasticity, depending on the range of environmental conditions the organism encounters,” Pigliucci said.

So, phenotypic plasticity is not a property of matter but a standard biological process, and it can be shaped by natural selection like other heritable characteristics. Nothing new here.

But then we do finally get back to evolutionary changes resulting from “properties of matter” such that the mechanisms are non-Darwinian.

Self-organization is another evolutionary force that some experts say whips up complex features or behaviors spontaneously in living and non-living matter, and these traits are passed on to offspring through the generations.

That a Lamarckian process of inheritance of acquired characters played an important role would be surprising indeed. Perhaps it is not so silly as that. Maybe the author is thinking of epigenetic changes that can be passed on. But that would still be only a minor variant of the standard Darwinian process — natural selection was conceived long before any specific rules about hereditary systems were identified. Genetic or epigenetic, if it is inherited and has effects on fitness, it can be subject to natural selection.

“A classic example outside of biology are hurricanes: These are not random air movements at all, but highly organized atmospheric structures that arise spontaneously given the appropriate environmental conditions,” Pigliucci said. “There is increasing evidence that living organisms generate some of their complexity during development in an analogous manner.”

A biological illustration of self-organization is protein-folding. A lengthy necklace of amino acids bends, twists and folds into a three-dimensional protein, whose shape determines the protein’s function. A protein made up of just 100 amino acids could take on an endless number (billions upon billions) of shapes. While this shape-shifting takes on the order of seconds to minutes in nature, the fastest computers don’t have the muscle yet to pull off the feat.

The mechanism that triggers the final form could be a chemical signal, for instance.

So are we relying purely on chance every single time a protein folds? Or is three dimensional structure consistent given a particular string of amino acids? If the latter (which it is, or we’d be dead), then this would imply that self-organizing that could go any which way is not the explanation. Rather, the string of amino acids and the conditions in which it folds (e.g., the chemistry of the cell) are heritable and have fitness consequences. Where might that “chemical signal” comes from, pray tell?

After this, there is more about phenotypic plasticity. There’s an example of butterflies with different colour patterns depending on season (so again, a question of how the environment affects gene expression during development — interesting and important to consider in evolutionary biology, but not a challenge to natural selection because the switch in colouration is adaptive).

The last example is of shorebirds called red knots which “can morph their phenotypes depending on their migration routes.”

When brought into captivity and placed in colder temperature environments, the shorebirds’ flight muscles and organs shrink to reduce heat loss. The birds pass on to offspring the capacity to make these changes.

Maybe this is an innocuous statement, like claiming “If people work out, they will get big muscles, and they pass on the capacity to get big muscles by working out to their offspring”. One could even say that some individuals’ offspring (say, Arnold Schwarzenegger’s) have a higher capacity to become muscular under conditions of heavy exercise than others’. But then, this wouldn’t be nearly as interesting as implying that soft inheritance is taking place.

Overall, this piece was really quite confused, mixing very different issues in a strange sequence, which is a shame in light of the good article they posted last week.

I still wonder what can be done to improve the accuracy of science reporting; “nothing” seems less and less like an acceptable answer.


Why are there transitional animals?

“Uh oh,” thought I upon seeing this headline from LiveScience: Greatest Mysteries: Why Are There Transitional Animals?

“This could go wrong in so many different ways,” I said to myself, “let’s see which one they went with”.

Much to my pleasant surprise, the story is actually pretty good. There’s a bit of the usual anthropomorphizing of natural selection (“it shows us how evolution could have tinkered with variation”), but overall it is a reasonable discussion of an interesting topic. I doubt the existence of so-called “transitional animals” counts as a “great mystery”, but this is made up for by an excellent quote from Jack Conrad of the AMNH in New York (where I spent a year as a post-doc).

“These early whales were basically playing the same game that crocodiles play: Wait for something to come get a drink and then pull it in the water for dinner,” Conrad said. “This is also the same game that early land vertebrates, early amphibians and early relatives of crocs and dinosaurs were playing. These animals weren’t necessarily ‘on their way’ to being anything; they were well suited to being exactly where they were.”

It is quite refreshing, after the dazed hype about human evolution over the past couple of weeks, to see a statement so on the mark.


Funny faces.

As noted in an earlier post, it is quite useful to have blogs, science news, and journal index searches all delivered to a single reader. Today I noticed an interesting juxtaposition of two news stories while skimming through my aggregated list of feeds. These two headlines were given in immediate succession (and from the same source):

Handsome By Chance: Why Humans Look Different From Neanderthals
Chance, not natural selection, best explains why the modern human skull looks so different from that of its Neanderthal relative.

Facial Attraction: Choice Of Sexual Partner Shaped The Human Face
Facial attractiveness played a major role in shaping human evolution, as studies on our fossil ancestors have shown our choice of sexual partner has shaped the human face.

These two studies aren’t mutually exclusive, of course. Neanderthals may have evolved their features by chance whereas human features evolved in response to sexual selection, but it’s amusing that such diametrically opposed explanations for facial features within the genus Homo — random genetic drift versus non-random mate choice — are given right next to each other in the news feed.


____________

The news stories are based on these articles:

Weaver, T.D., C.C. Roseman, and C.B. Stringer. 2007. Were Neandertal and modern human cranial differences produced by natural selection or genetic drift? Journal of Human Evolution 53: 135-145.

Weston, E.M., A.E. Friday, and P. Liò. 2007. Biometric evidence that sexual selection has shaped the hominin face. PLoS One 2(8): e710.


Dr. Jay on incomplete transcription.

If you don’t read the posts by John Timmer (“Dr. Jay”) on Nobel Intent, you should. He has posted some good summaries about the ENCODE project, the anemone genome, and today presents a very interesting discussion of incomplete transcription of inactive genes based on a paper in Cell. (Basically, even inactive genes may experience transcription initiation although this is not followed through to generate full transcripts). If you’re interested in accurate and accessible summaries of newly published findings, and especially if you want some realistic discussion of the significance of new genomics research, this is a good place to start.