The accurate language challenge, part III

Here’s one from the latest issue of The Scientist (emphasis added!).

Two hundred years after the birth of Charles Darwin, scientists are exploring one of the central questions of evolution: When organisms become more complex, by adopting the fittest traits for their environment, do those traits place constraints on further evolution? In other words, can complexity slow down the process of evolutionary change? ANDREA GAWRYLEWSKI visits scientists performing an ambitious experiment – involving at least 4,000 mice in the last several years alone – as they set out to find an answer.

CBC on the lack of funding for Genome Canada.

Last night on CBC, the National gave a report on the lack of funds for Genome Canada in the new budget by the Conservative government. My colleague Paul Hebert, who is the head of the massive international DNA barcoding project, was featured. This is just one of many areas in which Canada is a world leader but for which a lack of Genome Canada support may mean a huge negative impact.

Critics question lack of new funding for Genome Canada

Click to view

Conservative budget butchers Canadian science.

Canadian researchers are disproportionately productive and do an outstanding amount of science in light of the amount of funding they receive. That may change. It now seems that the Conservative government of Stephen Harper has taken even more steps to gut Canadian basic science.

Budget erases funding for key science agency
Carolyn Abraham
Globe and Mail January 29, 2009

The only agency that regularly finances large-scale science in Canada was shut out of Tuesday’s federal budget, putting at risk thousands of jobs and some of the most promising medical research, and forcing the country to pull out of key international projects.

“We got nothing, nothing, and we don’t know why,” said a stunned Martin Godbout, Genome Canada president and CEO. “We’re devastated.”

For the first time in nine years, Genome Canada, a non-profit non-governmental funding organization, was not mentioned in the federal budget and saw its annual cash injection from Ottawa – $140-million last year – disappear.

While research leaders have applauded the Conservatives’ plan to spend billions on construction and fixing old buildings on university campuses, they are mystified that the money to operate these facilities seems to be shrinking – particularly when U.S. President Barack Obama plans to double research funds in the U.S. over the next decade.

When President Obama comes to Canada, we can show him some nice labs with no one in them,” said Dr. Godbout, who compared the situation to supplying planes but no pilots or ground crews.

Dr. Godbout said he spent the day fielding calls from worried scientists and making calls to research funding partners in the United States and Europe saying that Canada would have to withdraw from a few key international projects – including some that were to be Canadian-led. Among them, he said, is the worldwide effort to sequence the genomes of 50 different types of cancer.

It’s not just big science. The Conservatives also plan to chop $87.2 million from the federal granting agencies in the next three years. They say this will not affect the amount provided to individual researchers, but their trend of focusing on (their own) ‘priority areas’ could very well mean that basic research will be gutted in the same manner as big science.

This is bad news. This is very, very bad news.

On the Origin of Species – Chapter 1

I am not planning any official blogging of the Origin (cf. Blogging the Origin), but I am currently reading it with a few students from my evolution course just for fun. We’re discussing it online and will be meeting to talk about it every week or two. I’m posting below what I posted in our discussion forum.

Chapter 1 – Variation Under Domestication

Darwin spends a lot of time discussing the fact that domestic breeds vary. This may seem pretty obvious to us, but it was an important set up for the idea that variation is common. Remember– no variation, no selection.

He also goes to pains to convince readers that domestic breeds (e.g., of pigeons) were all descended from a common ancestor. Again, this may seem obvious to us, but as he notes (p. 50), almost all breeders assumed that each breed was descended from a different wild ancestor. So, he is using these examples to establish common descent and branching.

Several important ideas already appear in the chapter:

1) Although he didn’t know how heredity works he knew it is crucial for his mechanism (p.33).

“Any variation which is not inherited is not important for us.”

2) Differences between modern organisms may be so great that it is difficult to imagine that they share common ancestors — he used the example of pigeons, which would be classified as different species if a taxonomist didn’t know they were domestic breeds because they look so different (p.44). And yet, all the information indicates that they are descended from the same ancestor species.

“Altogether at least a score of pigeons might be chosen, which if shown to an ornithologist, and he were told that they were wild birds, would certainly, I think, be ranked by him as well-defined species. Moreover, I do not believe that any ornithologist would place he English carrier, the short-faced tumbler, the runt, the barb, pouter, and fantail in the same genus”.

3) Selection is the main mechanism of change. Not crossing, not effects of environment, and so on (p.66).

“Over all these causes of Change I am convinced that the accumulative action of Selection, whether applied methodically and more quickly, or unconsciously and more slowly, but more efficiently, is by far the predominant Power.”

4) Selection is about the accumulation over many generations of almost imperceptibly slight changes (p.52-53). The emergence of breeds is gradual, probably too much to notice as it is occurring (p.62).

“We cannot suppose that all the breeds were suddenly produced as perfect and as useful as we now see them; indeed, in several cases, we know that this has not been their history. The key is man’s power of accumulative selection: nature gives successive variations; man adds them up in certain directions useful to him. In this sense he may be said to make for himself useful breeds.”

“But, in fact, a breed, like a dialect of a language, can hardly be said to have had a definite origin. A man preserves and breeds from an individual with some slight deviation of structure, or takes more care than usual in matching his best animals and thus improves them, and the improved individuals slowly spread in the immediate neighbourhood. But as yet they will hardly have a distinct name, and from being only slightly valued, their history will be disregarded. When further improved by the same slow and gradual process, they will spread more widely, and will get recognised as something distinct and valuable, and will then probably first receive a provincial name.

But the chance will be infinitely small of any record having been preserved of such slow, varying, and insensible changes.”

5) Selection is known to occur, at least with breeding (p.52, p.55).

“The great power of this principle of selection is not hypothetical.”

6) Most changes are ignored (neutral) or detrimental, but some are noticed and selected (p.61).

“Nor let it be thought that some great deviation of structure would be necessary to catch the fancier’s eye: he perceives extremely small differences, and it is in human nature to value any novelty, however slight, in one’s own possession. Nor must the value which would formerly be set on any slight differences in the individuals of the same species, be judged of by the value which would now be set on them, after several breeds have once fairly been established. Many slight differences might, and indeed do now, arise amongst pigeons, which are rejected as faults or deviations from the standard of perfection of each breed.”

7) Selection doesn’t require conscious effort. It can be unconscious (p.56).

“…a kind of Selection, which may be called Unconscious, and which results from every one trying to possess and breed from the best individual animals, is more important. Thus, a man who intends keeping pointers naturally tries to get as good dogs as he can, and afterwards breeds from his own best dogs, but he has no wish or expectation of permanently altering the breed.”

8) Large populations are best for selection (p.63).

“But as variations manifestly useful or pleasing to man appear only occasionally, the chance of their appearance will be much increased by a large number of individuals being kept; and hence this comes to be of the highest importance to success.

When the individuals of any species are scanty, all the individuals, whatever their quality may be, will generally be allowed to breed, and this will effectually prevent selection.”

9) If breeds are going to diverge, they must not interbreed (i.e., what we would now say means blocking gene flow) (p.64).

“In the case of animals with separate sexes, facility in preventing crosses is an important element of success in the formation of new races,—at least, in a country which is already stocked with other races. In this respect enclosure of the land plays a part.

On the other hand, cats, from their nocturnal rambling habits, cannot be matched, and, although so much valued by women and children, we hardly ever see a distinct breed kept up; such breeds as we do sometimes see are almost always imported from some other country, often from islands.”

Dr. Michael Majerus (1954 – 2009)

It is with deep regret that I follow Nick Matzke in announcing that Dr. Michael Majerus, an expert on industrial melanism and champion of the peppered moth as a prominent example of natural selection in the wild, has passed away after a short illness.

Dr. Majerus was a professor at Cambridge, and was a dedicated researcher and teacher. I did not know him personally, but I did have an opportunity to interact with him recently after inviting him to write an article on the peppered moth for Evolution: Education and Outreach. My experience was that he was very patient and cared greatly about getting the details right — indeed, the paper describes some of his own very careful research to counter critiques of the peppered moth example. I invite everyone to see the paper, which is a testament to Dr. Majerus’s dedication to excellent research and teaching.

He will be missed.

The accurate language challenge, part II.

Once again, the challenge is to translate sloppy shorthand into technically accurate explanations for what is going on…

As microbes evolve, they adapt to their environment. If something stops them from growing and spreading—such as an antimicrobial—they evolve new mechanisms to resist the antimicrobials by changing their genetic structure. Changing the genetic structure ensures that the offspring of the resistant microbes are also resistant.

http://www3.niaid.nih.gov/topics/antimicrobialResistance/Understanding/history.htm

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The accurate language challenge, part I.

Here is a little exercise I use in my evolution class. I post a segment of a news story that describes an evolutionary process in sloppy terms and then ask the students to translate it into language that accurately describes what is going on.

Here’s one from today’s Discovery News.

Lizards Evolved Quickly to Avoid Death by Ants

It takes some effort for fire ants to get under the hard scales of an unsuspecting lizard. When the insects finally penetrate the reptile’s fleshy core, the attackers inject a toxin that paralyzes their victim. Then, they tear the lizard to pieces, which they carry back to their nest.

It’s an unpleasant way to die, and one that at least one species of lizard is rapidly evolving to avoid. In just 70 years, according to a new study, eastern fence lizards in parts of the United States have developed longer hind limbs and new behaviors that help them escape the clutches of the venomous ants.

Have at it!

(Hint: Start your answer with “Within a population of lizards…”)

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Darwin’s note on higher and lower.

Here is a page from Darwin’s 1837 notebook. (Click for larger image)

In case you can’t read his handwriting (few can), it says

It is absurd to talk of one animal being higher than another. We consider those, when the cerebral structure / intellectual faculties most developed, as highest. A bee doubtless would when the instincts were.

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Worse than lower and basal.

Why can’t reports in the media accurately convey the basics of evolution? And why can’t scientists make a dedicated effort to clarify things whenever they give an interview? What hope is there for clarifying the most fundamental concepts when every story seems to reinforce misconceptions?

From the Discovery Channel:

Ancestor For All Animals Identified

A sperm-looking creature called monosiga is the closest living surrogate to the ancestor of all animals, according to new research that also determined animal evolution may not always follow a trajectory from simple to complex.

Yet another find of the study, published in the latest PLoS Biology, is that Earth may have given rise to two distinct groups of animals: bilaterians — animals with bilateral symmetry, like humans — and non-bilaterians, which include corals, jelly fish, hydra, unusual, often poisonous, creatures known as cubozoans, and other organisms.

Free-living, unicellular organisms called choanoflagellates, however, could be on every person’s family tree, so long as it was a gigantic one.

They determined that so-called “simple” and “lower” tier animals, such as corals and jellyfish, evolved in parallel to “higher” animals, like seemingly more complex insects and even humans. On the tree of life, monosiga then currently holds the root position for the latter group.

Please, let’s try to get this right from now on. No study reconstructing phylogenetic relationships between modern taxa tells you what the ancestor of those taxa was. It may provide some clues, but all species being examined are derived in some ways and primitive in others.

Trichoplax is not your ancestor.
You share a common ancestor with it.

No biologist who knows anything about evolution would suggest that evolution “always follow[s] a trajectory from simple to complex”. There is no such thing as “higher” and “lower”, though this pre-evolutionary idea apparently is hard to abandon.

And not every rearrangement of proposed evolutionary relationships is a revolution. Many of the deep nodes have been enigmatic for a long time, so it’s not a surprise when they move around based on improved information. Here is how I, an evolutionary biologist, react to each new molecular phylogeny that moves animal branches around:

“Neat. I wonder if it will hold up. It will be interesting to think about what this means in terms of major patterns.”

For a much better take on this new phylogeny written by someone with expertise, see Todd Oakley’s latest post. If we could just get more scientists to write blogs…

(Incidentally, the idea that the ancestors of animals were choanoflagellate-like organisms dates to the 19th century. I even parodied this well-known idea on a shirt).

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Lower and basal.

The story:

New Tree Of Life Divides All Lower Metazoans From Higher Animals, Molecular Research Confirms

The response:

“It is absurd to talk of one animal being higher than another” (Charles Darwin, 1837)

More information:

Understanding evolutionary trees

(By the way, Rob DeSalle, who is quoted in the story, was one of my postdoc advisors and he definitely understands phylogenies — but the story is pretty sloppy nonetheless)