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February 15, 2014

Darwin Day 2014 -- North Dakota State University takes the cake

DarwinDaySong.jpeg

Wow! I can't decide whether I'm more impressed by:

* the guy in the pickup truck who saw us carrying the cutout photo of young Darwin and asked "Is that [W.D.] Hamilton?"
* the evolution-themed parody of John Lennon's "Revolution", composed and performed by a dean who, like God, may have "an inordinate fondness for Beatles".
* the wildly popular herpetology petting zoo (I should have taken a photo), or
* the "Hall of Biodiversity" (a wide range of interesting materials from campus natural-history collections, showing butterfly mimicry, comparing mammoth with mastodon teeth, using C4 photosynthesis as an example of parallel evolution, etc.) set up in the student center next to the auditorium where I gave my talk on "Darwinian Agriculture: Evolutionary Tradeoffs as Opportunities" and the lobby area (shown) where they sold Darwin-Day tee shirts and served cake.

But the cake I made for Darwin's 200th birthday was better.

July 10, 2013

Fake scientific journals: a boon to "intelligent design"?

Over the years, intelligent-design advocates have only published "12 peer-reviewed articles from scientific journals that are claimed to support intelligent design," none which stands up to critical analysis. That analysis is more important than mere numbers, although it's worth noting that there are more than 12 papers on evolution published every day. However, the recent proliferation of fake "scientific journals," which will publish anything for money, may lead to a big increase in fake intelligent-design publications. We'll see.

For example, Scientific Research Publishing just invited me to join the editorial board for its open-access journal, Advances in Reproductive Sciences. Looks like an invitation sent at random, since I have no expertise in that field and since the email (from Editorial Assistant "Christine") was totally generic. One way to assess journals is by the qualifications of people on their editorial board, but that breaks down if journals lie about who's on their board. For example, I found this discussion of Scientific Research Publishing on the James Randi Educational Foundation web site:

"Oddly, I've been searching through the editorial board on the JBSE and haven't seen anyone listed there actually have it on thier own CV. ETA: Alright. It's getting a bit more strange. I saw they had listed a Dr. Sridharan Devarajan, from stanford. on the editorial board. however, this person is currently a PhD student. Further, he has listed on his cv that he is an "ad hoc" reviewer. hmmm.... "

I can't vouch for the accuracy of the comment, of course. This article in The Hindu quotes a professor listed as "editor-in-chief" of a journal published by the OMICS group, denying that he ever accepted that position. The article links to this lengthy list of suspect publishers, which includes both OMICS Group and Scientific Research Publishing.

There's more on fake scientific journals and fake scientific meetings in the New York Times and Nature.

The Scientific Research Publishing web site says they publish 200 journals and it looks like most of them were started this year. I guess it's too much work to look for qualified board members when you're starting that many journals all at once. Interestingly, the email I got didn't mention reviewing manuscripts as one of the responsibilities, but did mention "a valuable credential for tenure and promotion." They charge $600 to "process" a manuscript. I wonder if they charge for this "valuable credential."

Committees responsible for hiring, tenure, and promotion are supposed to evaluate publications, not just count them, although busy people aren't always as thorough as we should be. I can't imagine anyone getting hired at a major university based solely on publication in fake journals (or low-quality journals, even if they're not deliberate scams) and invited talks at fake conferences. But, when I was a research scientist for USDA, we were expected to publish at least one paper every year. This wasn't a problem for colleagues publishing low-quality research in journals whose "peer review" process overlooked even obvious errors (like including the same citation twice in a five-paper bibliography). But one of my best (and most-cited) colleagues was put on probation when he missed a year, despite publishing in top journals right before and right after the period in question. Years ago, a postdoc from another country told me that US Immigration uses citations, not mere publication, to evaluate scientific credentials of visa applicants. Citation analysis has limits, but it's an improvement over just counting publications.

See "Recent Comments" for reader reactions to my previous posts on fake scientific meetings and similar science scams, including two claiming these conferences are legit. One commenter used a pseudonym and the other is worth Googling.

January 28, 2011

Also this week...

Defeating Creationism in the Courtroom, But Not in the Classroom
Only 28% of high school biology teachers are doing their job. See comments by PZ.

Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World Nabokov's hypothesis was apparently right, "A novel method is used to estimate ancestral temperature tolerances using the limits of distribution ranges of extant organisms", etc. See comments by Carl Zimmer.

Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity Evolution of a new function for the key metabolite, NADPH

Leaving home ain't easy: non-local seed dispersal is only evolutionarily stable in highly unpredictable environments Spreading seeds widely won't usually get them to consistently better spots, so it's more of a bet-hedging mechanism.

Importance of single molecular determinants in the fidelity of expanded genetic codes The latest on making organisms that use a DNA stop codon to encode an amino acid not normally found in proteins

Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b Using DNA to track human migration history

The Newest Synthesis: Understanding the Interplay of Evolutionary and Ecological Dynamics Ecological changes can drive evolution, but what about the reverse?

Oceanic rafting by a coastal community
I still don't believe that's how camels got to Australia.

Evidence of parasitic Oomycetes (Peronosporomycetes) infecting the stem cortex of the Carboniferous seed fern Lyginopteris oldhamia

Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life
We can't grow these newly discovered microbes in culture, but we can classify them as a new branch based on their DNA, and we can use their DNA sequences to make fluorescent probes to label them for microscopy.

Oxytocin promotes human ethnocentrism

December 15, 2010

One evolutionary biology lab's publications in one year match "intelligent design's" 5-year total

In one of my first posts, I surveyed the scientific literature and found that there are thousands of scientific papers published on evolution every year, strong evidence against the long-running claims of evolution-denialists that scientists are rejecting evolution. But would it be rude to compare a single evolutionary biology lab's research productivity for one year to "intelligent design's" total for five years?

Denison lab: 4 papers published in 2010, all with original data.
They claim: 0 in 2010 (as of today), 2 in 2009, 0 in 2008, 0 in 2007, 2 in 2006...
... so 4 papers in 5 years (<1/yr), 0 with original data.

Their pathetic publication record confirms the criticism their list was intended to refute, namely, that intelligent design advocates don't publish much because they "don't have scientific data." Here's our list:


4) Ratcliff, W.C., R.F. Denison. 2010. Individual-level bet hedging in the bacterium Sinorhizobium meliloti. Current Biology 20:1740-1744.
Perhaps because the duration of starvation is often unpredictable, these bacteria "hedge their bets" by dividing into one starvation-resistant "persister" and one more-active "grower." See this blog post.

3) Oono,R., R.F. Denison. 2010. Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids. Plant Physiol. 154:1541-1548.
Rhizobia provide nitrogen more efficiently (more N per CO2 respired) in hosts that make the nitrogen-fixing bacteroid form swell up and lose the ability to reproduce, relative to the same rhizobial strains in hosts where bacteroids aren't swollen. See this blog post.

2) Denison, R.F., J.M. Fedders, B.L. Harter. 2010. Individual fitness versus whole-crop photosynthesis: solar tracking tradeoffs in alfalfa. Evolutionary Applications 3:466-472. By disrupting solar tracking and measuring effects on photosynthesis, we showed that the overall effects of tracking on photosynthesis can be negative. So why do they do it? See this blog post.

1) Oono,R., I. Schmitt, J.I. Sprent, and R.F. Denison. 2010. Multiple evolutionary origins of legume traits leading to extreme rhizobial differentiation. New Phytologist 187:508-520.
Legumes have evolved the ability to impose bacteroid swelling (shown above to increase nitrogen-fixation efficiency) repeatedly. See this blog post.

Our small lab should outperform all of "intelligent design" again in 2011, as the following have been already published or accepted:

Denison, R.F. 2011. Past evolutionary tradeoffs represent opportunities for crop genetic improvement and increased human lifespan. Evolutionary Applications (already on-line). See this post.

Kiers, E.T., R.F. Denison, A. Kawakita, E.A. Herre. 2011. The biological reality of host sanctions and partner fidelity. 2011. Proc. National Academy of Sciences (already on-line). Four of us, each studying a different mutualism, critique this paper, one of many that draws incorrect conclusions from modeling that ignores the tragedy-of-the-commons created by multiple symbionts per host, as I've discussed previously. Here's their response.

Oono, R., C.G. Anderson, R.F. Denison. 2011. Failure to fix nitrogen (N2) by nonreproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proc. Roy. Soc. B (already on-line). Inside the root nodules of some legume species, rhizobial bacteroids (the differentiated form of these bacteria, which convert atmospheric nitrogen into a form the plant can use) have lost the ability to reproduce. If these plants just cut off resources to nonreproductive bacteroids that fixed too little nitrogen, that would have no direct effect on future generations of rhizobia. But Ryoko Oono and Carolyn Anderson showed that pea and alfalfa, two examples of such legumes, can reduce the reproduction of the bacteroids' still-reproductive clonemates in the same nodule, perhaps by cutting off resources to an entire nodule when it doesn't fix nitrogen.

Ratcliff,W.C., R.F. Denison. 2011. Bacterial persistence and bet hedging in Sinorhizobium meliloti. Communicative and Integrative Biology (abstract already on-line). This is a follow-up to Will Ratcliff's recent paper showing that starving rhizobial bacteria bet-hedge by splitting into one high-resource "persister" (which can survive long-term starvation) and one low-resource but more-active "grower." New data in this paper show that the persister cells are resistant to an antibiotic that kills growing cells, and that they have lower rates of protein synthesis, at least for the green-fluorescent protein.

Hendry, A.P., M.T. Kinnison, M. Heino, T. Day, T.B. Smith, G. Fitt, C.T. Bergstrom, J. Oakeshott, P.S. Jørgensen, M.P. Zalucki, G. Gilchrist, S. Southerton, A. Sih, S. Strauss, R.F.Denison, and S.P. Carroll. 2011. Evolutionary principles and their practical application. Evolutionary Applications (in press). What can evolutionary biology contribute to conservation biology, agriculture, and medicine? This synthesis paper from the Applied Evolution Summit, held on Heron Island in January finds some useful generalizations.

My research has been and is supported by the National Science Foundation, but the opinions expressed here are my own.

July 17, 2010

Directed evolution versus intelligent design of enzymes

"How have all those exquisite adaptations of one part of the organisation to another part, and to the conditions of life, and of one distinct organic being to another being, been perfected? We see these beautiful co-adaptations most plainly in the woodpecker and missletoe; and only a little less plainly in the humblest parasite which clings to the hairs of a quadruped or feathers of a bird; in the structure of the beetle which dives through the water; in the plumed seed which is wafted by the gentlest breeze; in short, we see beautiful adaptations everywhere and in every part of the organic world." -- Charles Darwin
Evolution denialists often claim that these adaptations must have come from an Intelligent Designer, who has apparently been too busy lately (protecting pedophile priests, maybe, or working to block gay marriage?) to come up with any new designs. They claim that natural selection (nonrandom proliferation of random variants) isn't up to the job.

But intelligent human designers are increasingly relying on processes similar to natural selection. The latest issue of Science discusses two examples of the use of selection-like processes for developing useful enzymes. One paper explicitly calls their approach "directed evolution." The other doesn't use the term, but what would you call generating billions of randomly varying designs in a computer and selecting those that meet certain criteria? Sounds like selection to me. In neither case did the researchers rely only on natural-selection-like processes. Instead, they used some combination of intelligent design and selection from among random variants. But nonrandom selection from among random variants was a key contributors in each case, solving problems beyond the reach of human reason or intuition.

June 25, 2010

Evolution meetings in Portland

The Society for the Study of Evolution, the Society of Systematic Biologists, and the American Society of Naturalists are meeting together over the next few days, in Portland, Oregon. I'm not going this year, unfortunately, but my grad students Ryoko Oono and Will Ratcliff will both be speaking.

Once again this year, there are no sessions scheduled on atheism, pornography, abortion, etc., just evolution. It's almost as if evolutionary biology were a science, maybe even a branch of biology! Reminds of a job fair long ago, where they told me "ecology" was too broad a specialty, but "biology" was OK.

May 21, 2010

Creation disproved?

If evolutionists want to end the arguments all they have to do is, get their brilliant heads together and assemble a 'simple' living cell. --creationist comment, 2007
Somehow, I doubt that the simple living cell assembled by Venter and colleagues will end the arguments. (Discussion at Pharyngula and elsewhere.) First, we're still a ways from making a working cell "from scratch." Venter's group used an existing cell, minus its DNA. It probably won't be too long before well be able to fill that gap (if anyone wants to bother), using membranes, ribosomes, etc. made in the lab without the use of living cells. But I'd be very surprised if we succeeded in designing and making life in the lab without using information from existing life within the next 50 years. Venter used the complete DNA sequence from another bacterium. But even if he'd designed the whole genome from scratch, the idea of using DNA as the hereditary material would be "borrowed" from existing life.

Are we smart enough to invent a totally new form of life? A computer virus that mutates in response to selection imposed by spam filters might qualify. So might a self-reproducing robot. In both cases, they would need special conditions (availability of computers or robot parts) to reproduce, but that's true of most living things. Could we design a life-form that could reproduce and evolve without using any materials produced by existing life-forms? Not anytime soon, I bet.

Could we, instead, create the conditions under which such a new life-form would arise and then evolve? For example, suppose we set up a thin metal plate with billions of cell-size holes through it (dimensions chosen so that macromolecules would have more chance to interact with each other than if they were floating in a large volume of water), then manipulate the chemical conditions on the two faces to provide a potential source of chemical energy. Throw in some of the organic molecules we know can arise from nonliving processes, and wait. Or something like that.

Continue reading "Creation disproved?" »

March 5, 2010

Evolution via less-fit intermediates

A central hypothesis in my forthcoming book, "Darwinian agriculture: where does Nature's wisdom lie?" is that past natural selection is unlikely to have missed simple, tradeoff-free improvements. This implies (as discussed in a recent post on drought-tolerant wheat) that tradeoff-blind biotechnology is less likely to succeed, relative to crop-improvement methods that consider tradeoffs, as long as biotechnology is limited to simple changes, like increasing the expression of an existing gene.

More complex improvements (those whose evolution would require a series of steps) are another story, however. Just because some hypothetical horse would kick ass, if it did evolve, doesn't guarantee that it will evolve. The problem is that you can't get from genotype A to some very different genotype Z, except through one or more generations of individuals with intermediate genotypes.

It's fairly easy to get from A to Z, provided that B is at least as fit as A, while C is at least as fit as B, and so on. This can be the case, as shown by experiments on the five-step evolution of antibiotic resistance, discussed in a previous post. But is this the only way a population can evolve a superior genotype? Or does evolution sometimes reach new heights (faster-flying birds, scummier pond scum, etc.) through intermediates that are significantly less fit?

Evolution via less-fit intermediates would expand evolution's options, making it even harder for biotechnology folks to come up with something missed by evolution. And that's what this week's paper seems to show.

"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness" was recently published in Nature by Margarita Meer and colleagues.

Continue reading "Evolution via less-fit intermediates" »

August 29, 2009

Peacock comment

Most of the "comments" I get on older posts are commercial spam, which I delete. But if you're interested in a creationist comment on Dave Wisker's guest post on peacocks, here it is. It seemed to be original rather than cut-and-paste, so I approved it, but did add some comments of my own.

May 8, 2009

"If evolution is true, why are there still chimps?"

I once heard PZ reply to this popular creationist question by pointing out that, although many Minnesotans are descended from Norwegians, there are still Norwegians. This isn't really a good analogy, however, because Minnesotans and Norwegians aren't separate species. We know this because they can interbreed, producing healthy children. At the end of this post I suggest a better answer, indirectly inspired by this week's paper.

Two of evolutionary biology's central questions are: how do species change over generations? and how does one species split into two? We have many detailed examples of small evolutionary changes occurring over days (in bacteria) or years (in animals and plants), so one would have to be very close-minded to deny major evolutionary change over millions of years. But major evolutionary change is not enough, by itself, to split one species into two. One subpopulation within a species must change, while the rest of the species either stays the same or changes in different ways. This divergence cannot happen if the two subpopulations continue to interbreed at high rates. In other words, speciation requires some reproductive isolation.

Often, reproductive isolation is a byproduct of geography. After a few individuals (or a pregnant female) cross a mountain range or are blown from the mainland to an island, they no longer interbreed with their ancestral population. Over many generations, random genetic drift or nonrandom natural selection can change the isolated population enough that they can no longer produce healthy offspring with the original population, even if they come back into contact.

Sometimes speciation can occur without a major geographic barrier, but reproductive isolation is still required. This week's paper shows that this has happened and is still happening in Europe.

"A continuum of genetic divergence from sympatric host races to species in the pea aphid complex", by Jean Peccoud and others, was just published online in the Proceedings of the National Academy of Science.
aphid.jpg
Photo by Jean Peccoud

Continue reading ""If evolution is true, why are there still chimps?"" »

March 28, 2009

Facts and theory in Coyne’s “Why evolution is true”

“But if you believe that primates and guinea pigs [both of which have mutated, nonfunctional versions of a gene for making vitamin-C] were specially created, these facts don’t make sense. Why would a creator put a pathway for making vitamin C in all these species and then inactivate it? Wouldn’t it be easier simply to omit the pathway from the beginning? Why would the same inactivating mutation be present in all primates, and a different one in guinea pigs? Why would the sequences of the dead gene exactly mirror the pattern of resemblance predicted from the known ancestry of these species? And why do humans have thousands of pseudogenes [DNA sequences very similar to genes that are functional in other species, but with mutations that make them inactive] in the first place?” – Jerry Coyne, Why Evolution is True

I have been reading and enjoying “Why evolution is true”, by Jerry Coyne. Here are some thoughts on what I’ve read so far.

Continue reading "Facts and theory in Coyne’s “Why evolution is true”" »

November 21, 2008

November 21

Until I finish my book, Darwinian Agriculture, I am cutting back detailed posts to once or twice a month, but here are some links to papers that looked interesting this week.

Sustaining biodiversity in ancient tropical countryside
"arecanut palm (Areca catechu) production systems retain 90% of the bird species associated with regional native forest"

Selfish Genetic Elements Promote Polyandry in a Fly

[This "selfish gene" on the X chromosome refuses to share sperm with a Y chromosome. Female fruitflies mate with more males when more of them have this gene.]

Frequency-dependent selection maintains clonal diversity in an asexual organism

Reproductive constraint is a developmental mechanism that maintains social harmony in advanced ant societies

Finally, someone left a comment on an earlier post that used an out-of-context quote to claim evolutionary biologists are hiding from the fossil record. The truth is that fossils are less important to evolutionary biology today only because their contribution is diluted by new sources of information, especially comparisons of DNA sequences among species. But fossils are still a valued source of information. Here are two papers on fossils published this week in major journals. (How many papers did the "intelligent design" folks publish in major journals this week? This year? None?)

A new stem turtle from the Middle Jurassic of Scotland: new insights into the evolution and palaeoecology of basal turtles

Variation in Evolutionary Patterns Across the Geographic Range of a Fossil Bivalve

June 18, 2008

Guest blog: The Peacock's Tale

This week's post is by Dave Wisker, a graduate student in Molecular Ecology at the University of Central Missouri.

It's the creationist's dream. If actual evidence of creation is too much to hope for, how about a peer-reviewed paper in a respected journal overturning one of the icons supporting a major element of Darwin's theory?. Sexual selection in peafowl is definitely one of those icons. There appeared to be ample empirical evidence that peahen's preference for more elaborate trains on their mates has led to the spectacular male tail displays we see today. A series of papers in the 1990's by behavioral ecologist Marion Petrie and others seemed to solidly support this, and there is also evidence that elaborate tails may indicate good genes (Petrie et al, 1991; Petrie and Williams, 1993;.Loyau et al, 2005a). This, in itself, is a challenge to an older idea that the peacock's tail shows how arbitrary female preferences can be amplified to extremes by a "runaway"? process (Fisher, 1958). But, whatever their evolutionary origin, the preference itself has rarely been questioned.

However, a recent paper published in Animal Behaviour (http://tinyurl.com/4t69v5), "Peahens do not prefer males with more elaborate trains"?, challenges the conventional wisdom.

Continue reading "Guest blog: The Peacock's Tale" »

May 7, 2008

Real vs. fake controversy

I liked this essay comparing areas in evolutionary biology where there is genuine controversy -- i.e., where people who are actually collecting data and publishing on a topic disagree -- vs. the phony controversies imagined by creationists. Group selection may still almost qualify as a controversy, a question I may address in a later post, but age of the earth, common ancestry of all species (at least those studied so far!), and the power of natural selection to solve difficult problems are not at all controversial among those actively publishing on related topics.

The question of how much exposure high school students should have to genuine scientific controversies seems a bit more complex to me. I agree that helping students get enough of the basics to understand active controversies in any depth is a big challenge. On the other hand, I've been amazed how many high school students (and their parents) think that the only definition of "research" is looking up information in a library or on the web. If we want students to understand that scientific research is an exciting, ongoing activity, some kind of exposure to areas where scientists disagree seems essential. Areas of research that are easier to understand, like the mindless screening of drugs, don't convey the intellectual excitement of real science.

Here's a seminar class I've thought about for either high school seniors or first-year college students. First, let's set the minimum standard for a scientific controversy as: at least two conflicting points of view, each represented by data-containing papers from at least two nonoverlapping groups, in journals with an impact factor of at least 1.0. Each week we consider one question, such as:
1) What causes AIDS?
2) What is killing amphibians around the world?
3) How old is the earth (within 10%, say)?
4) What living species is the closest relative of chimpanzees?
Students get points for showing that each topic was controversial, at least at one time, with a big bonus for whoever shows controversy most recently. Then we could make a time-line, showing when each question was settled (pending new data, of course!).

November 19, 2007

Biological evolution vs. word games

Each generation tends to resemble the previous one, so evolution of whales from land animals, for example, took many generations. One limitation on the power of natural selection is that each generation must be viable. Some creationist suggested that the problem is analogous to "evolving" a sentence one letter at a time to make a substantially different sentence, while requiring that each intermediate step be a valid sentence. The Mosquito Eater has solved this challenge. Cool!

But we no longer need to rely on imperfect analogies to biological evolution. Molecular tools now make it possible to explore multistep evolution experimentally, as I discussed in an early post.

September 6, 2007

Evolution avoidance syndrome

That's the title of an essay by my colleague Scott Lanyon. He notes that "development" refers to changes within an individual, whereas changes in the genetic composition of a population are known as "evolution." Apparently some public officials were afraid to say that a fish population could "evolve" resistance to a newly arrived pathogen, so they say they hope resistance will "develop." This is confusing, because individual susceptibility to pathogens can develop, increasing or decreasing with age, but that's not what they were talking about.

I used to run into a similar problem when I worked in an agronomy department. Some of the people I interacted with would say that an herbicide had "broken down", when actually the weed species it once killed had evolved resistance to it. The change was in the weeds, not in the pesticide. This misuse of the English language is particularly harmful because herbicides do break down (chemically degrade), which is usually a good thing; we don't want them polluting lakes, for example.

Populations evolve, but don't worry, fish and weeds didn't evolve from apes.

July 30, 2007

Didn't mean to be unKIND

Reminder: generic comments on evolution not tied to a particular post, unsupported assertions, tirades, philosophical or religious discussions, etc. are welcome in the comments section of the Troll Refuge but not elsewhere. Repeat offenders will be banned. If anyone feels like arguing with a creationist, who claims that evolution can't create new KINDS -- is this an acronym, or is he just shouting? -- I just moved his comments there, along with my response.

Also in the Troll Refuge, Hermione Granger, founder of Save the Trolls, weighs in on the faith vs. skepticism debate.

April 19, 2007

This year in intelligent design

There are hundreds of papers published each month whose authors find evolution useful in explaining their results. One would think that, if "intelligent design" has any scientific merit, there would be a significant number of papers each month presenting evidence of supernatural intervention by an intelligent designer. Surely the many religious scientists, in particular, wouldn't fail to publish results that turn out to support intelligent design, even if that wasn't the original focus of their research.

However, I haven't seen even one paper on intelligent design so far this year that meets the basic scientific criteria in my first post. Maybe I've missed some? Let's check the Discovery Institute web site.

Continue reading "This year in intelligent design" »

March 27, 2007

Evolution of color vision: transgenic mice see red

This week’s paper, "Emergence of novel color vision in mice engineered to express human cone pigment", by Gerald Jacobs and colleagues at UC Santa Barbara and Johns Hopkins Medical School (Science 315:1723), is yet another experimental study that increases our understanding of how repeated cycles of natural selection, each producing a fairly small change, can lead to adaptations that may seem irreducibly complex.

Most humans have three different photopigment color sensors, as do our closest relatives. Many other mammals, including mice, have only two. Three-color vision is useful for many purposes, from identifying higher-protein leaves to eat (Nature 410:363) to telling which wire to cut to disarm the nuclear bomb buried under the stadium. But eventual usefulness isn’t enough for a trait to evolve. If a series of steps is required, each step must be beneficial, or at least not lethal. Such a series of steps has been worked out for the evolution of optically sophisticated eyes from light-sensitive spots (Proc. Roy. Soc. B 256:53), but what about color vision?

Continue reading "Evolution of color vision: transgenic mice see red" »

March 10, 2007

Troll refuge may prevent local extinction

I reserve my blog-given right to delete off-topic comments -- except in this Troll Refuge. "Comments" whose only purpose is to link to a commercial or crackpot site will generally be deleted everywhere. This is a free service to people who may not realize they are crackpots.

Comments immune from deletion outside the Troll Refuge are either:
1) comments on the particular paper-of-the-week, or
2) suggestions for papers to discuss that meet the criteria in my first post.

"But", you may say, "I've got this great proof that evolution is all wrong! This scientist said something that could be interpreted as inconsistent with some aspect of evolutionary theory! That proves that both versions of the creation story in Genesis (cattle and trees created before and after humans) are literally true, doesn't it?"

If the scientist said it in a peer-reviewed paper published in the last month and containing new data, you can suggest it as a paper of the week. Otherwise, post your proof here in the Troll Refuge.

The comments section for this entry is also the place to whine about censorship, or to complain about my failure to delete someone else's comment that you think is off-topic. Off-topic comments attached to other entries are subject to deletion, or, if particularly amusing, transfer to this troll refuge, possibly with appropriate editing. Trolls repeatedly posting outside the refuge will be banished.

Troll hunters are welcome in the refuge, too. This may seem cruel, but we need to keep the population below carrying capacity. However, no firearms will be allowed, only sticks and stones. And words, of course.

March 8, 2007

Experiments with "fitness landscapes" explain evolution of interacting genes

A reader asked an interesting question about the difficulty of coordinated evolution of groups of genes. Although I welcome comments and questions, I won't usually have time for detailed responses. and I'd already discussed one paper this week. But then Huxley brought in a recent issue of Nature he'd been chewing on, and there it was: "Empirical fitness landscapes reveal accessible evolutionary paths" (Nature 445: 383-386). So I guess I should take this dog-given opportunity to talk about the evolution of multiple interacting genes. The Nature paper is a review article with no original data, so isn't eligible for my regular weekly paper discussion, but maybe it's OK as a bonus paper, especially since the most interesting papers it discusses were published within the last year and they do contain original data.

The exciting thing about these papers is that people are starting to use molecular methods in experiments that solve "you can't get there from here" problems in evolutionary biology.

Continue reading "Experiments with "fitness landscapes" explain evolution of interacting genes" »

February 14, 2007

Evolution triumphs over photosynthesis

In general, I don't want to waste time responding to tired old creationist criticisms of evolutionary theory that have already been refuted elsewhere (such as here or here) -- criticisms backed by new data would be another story -- but I do need to address one issue that could undermine my ability to find a paper to discuss each week. Some creationists have suggested that scientists are increasingly rejecting evolution. Actually they've been saying this for a long time. Is my paper pipeline drying up?

Continue reading "Evolution triumphs over photosynthesis" »