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Wednesday, December 24, 2008

Top Ten Intelligent Design Creationist Stories

 
Denyse O'Leary is one of the best of an excellent group of science journalists.1 When she selects her top ten science stories of 2008 it's time to pay attention, especially since these are stories about Intelligent Design Creationism [The top ten Darwin and Design stories of the year.

Here's the list ...
The Altenberg 16
Atheists and Agnostics Defend ID
Expelled #1 Political Documentary of 2008
Louisiana Academic Freedom Act
Biologic Institute Releases Stylus: A System for Evolutionary Experimentation
A Molecular Clutch Discovered in the Flagella
Royal Society Expels Director of Education
Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome
Have Cosmologists Lost Their Brains?
Design-based Biomimetics Yields Tangible Results
What a sad list.


1. Not. I wonder what George Johnson thinks of science journalists like Denyse O'Leary?

The "Best" of Genetics Science Writing from New Scientist

 
The blogosphere is discussing the conflict between scientists and science journalists. The issue is not whether science journalists can write for the general public—I take that as a given—it's whether what they write is scientifically accurate. Do articles by science journalists fairly represent the state of science?

New Scientist has risen to the challenge by listing it's top ten article on genetics [Genetics: Top 10 articles from 2008.

Here's the list of titles. Judge for yourselves.
Me and my genome
DNA dating: Can genes help you pick a mate?
Genes make mice squeal during sex
Are political leanings in the genes?
Cloning 'resurrects' long-dead mice
Genetically modified humans: Here and more coming soon
MicroRNAs: The cell's little emperors
Solar-powered sea slug harnesses stolen plant genes
Cancer special: Living with the enemy
Goldmine bug DNA may be key to alien life



Monday, December 22, 2008

Webpages as Graphics for Sandwalk

 
Here's the Webpages as Graphics for this blog. I have no idea what this means.




Who the Heck Is George Johnson?

 
A few weeks ago I wrote about Epigenetics at SEED. The article in SEED was written by a scientist who wants to change evolutionary theory in order to accommodate epigenetics. I pointed out that this was a poorly written article. One of the worst problems was the definition of epigenetics, which was broad enough to include the kitchen sink.

Abbie Smith picked up on this on her blog ERV. She agreed that the SEED article was not helpful [ew... epigenetics in SEED...].

Along comes someone named George Johnson. He interprets Abbie's criticism of the science, and mine, as a rant against science journalism. Well, he's right, even though in this case it's science journalism being written by a scientist. Apparently science journalists (I assume George Johnson is one) are very sensitive about criticism from scientists. Apparently science journalists are very good at what they do ... how dare scientists criticize what they write about science!!!

Watch George Johnson make a fool of himself on this bloggingheads video with John Horgan. Johnson reads my name from the ERV posting but it seems he didn't bother to read my posting. If George Johnson has the courage to show up here I'll be happy to explain to him why this particular SEED article is bad. He's welcome to read all my other criticisms of science journalism and and attempt to defend the science journalists.

Pay close attention to Johnson's comments when he reads the passage from Abbie's blog. It's clear that he doesn't know what chromatin is and he doesn't know what epigenetics is. On the other hand, he is certain that Nicholas Wade, who writes about molecular biology, is a great science writer. How would George Johnson know this? Johnson may be able to tell whether Nicholas Wade is a good writer but he sure isn't in a position to judge whether he's a good science writer since the most important thing about science writing is accuracy and Johnson knows nothing about molecular biology.

This may be one of the biggest problems with science writers. They can't tell the difference between science and writing. And they don't like it when scientists point this out to them.






Friday, December 19, 2008

Name That Research Scientist

 
I'd love to know the name of this "research scientist" and the name of the pharmaceutical company he works for.

From DonaldM at Uncommon Desent:
Today, I had the privilege to have lunch with a research scientist who works in the area of bio-pharmaceuticals for a pharmaceutical company. He told me about their research with proteins and genes that enable them to develop products that alleviate or cure a wide range of diseases at the cellular level. Of great value to the research they do was the Human Genome Project because it made available the entire database to whoever needed it. That information enabled them to move several projects forward.

He knew from our conversation that I had been involved in the Intelligent Design/Evolution debate, so I asked him what role evolution played in all thier research. Now, this is a research facility that is carrying on a huge number of projects across a number of areas in cellular biology, bio-chemistry, hemotology, oncology and other related areas. He said that evolution plays no role whatsoever in their research and that evolutionary theory doesn’t make one whit of difference to the outcome of any of their research projects and never has. To clarify, I said, "so the heuristic value of evolutionary theory to your biological research is…." and he answered "Nil!".


Center for Inquiry World Congress 2009

 

The Center for Inquiry's 12th World Congress:
Science, Public Policy, and the Planetary Community
April 9-12, 2009
Bethesda, MD Hyatt Hotel (just outside of Washington, DC)


2009 marks the bicentennial of both Charles Darwin's and Abraham Lincoln's birth and the 150th anniversary of the publication of On the Origin of Species. There can be no more fitting opportunity to discuss and consider the appropriate relationship between science and public policy. Please join us as scientists and scholars from around the world analyze the role of science, explain how it works, explore its connection to public policy, and examine its significance for the global community.

Speakers
Norm Allen
Mona Abousenna
Tom Beauchamp
Roger Bonnet
David Contosta
Austin Dacey
Tarek Fatah
Barbara Forrest
Ren Fujun
Christopher Hitchens
Pervez Hoodbhoy
Leo Igwe
Philip Kitcher
Lawrence Krauss
Paul Kurtz
Ronald A. Lindsay
Elizabeth Loftus
John C. Mather
Joe Nickell
James Randi
Michael Ruse
Armadeo Sarma
Patricia Scott Schroeder
Drew Shindell
Eleanor Smeal
Eddie Tabash
Floris van der Berg
Toni Van Pelt
Ibn Warraq
Mourad Wahba
Richard Wiseman




Student Perceptions of "The Spandrels of San Marco"

 
Hopeful Monster asked his senior biology majors to read "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme." [Student perceptions of San Marco].

I think he was disappointed.


How Women Got Their Menopause

The December 13 issue of New Scientist has an article about the evolution of menopause in humans [Are daughters-in-law to blame for the menopause? ]. The author is Alison Motluk, the Toronto corresponent for New Scientist.

She begins with ..
IT FLIES in the face of natural selection, yet in humans it seems fixed and universal: at around age 50, not far past the midpoint of life, normal healthy women lose their capacity to bear children. Following a decade of gentle winding down, the whole reproductive system screeches to a halt. It is as though, after a few years of wearing bifocals, all women suddenly went blind.

Menopause is a mystery. It leaves women with 20, 30, perhaps even 50 years of life - squandered time in evolutionary terms, because no further genes can be passed on. Yet the selection pressure for menopause must have been strong: there are no known pockets of women around the world who do not go through it. All the evidence suggests menopause has been around a long time, and that the age at which it hits has changed little. Increased longevity seems not to have budged our closing hours. Nor, apparently, has lifestyle; it hits hunter-gatherers at pretty much the same age as hip New Yorkers.
The search for an adaptive explanation for menopause has been going on for over fifty years.

The most common just-so story is called the "Grandmother Hypothesis." It imagines a time in the distant past when humans females were fertile until the day they died, which for 75% of women who survived childhood was before the age of 30 according to a recent study. A mutation arose in one individual and the effect was to induce menopause, or sterility, at about age 50. This new mutation proved to be so beneficial that it spread throughout the species. Today every woman undergoes the pain and frustration of menopause.

Why was it so beneficial? Because post-menopausal women whose partners were still alive could invest their time in looking after their grandchildren instead of having more children of their own.

To its credit, the New Scientist article reviews the latest work on the Grandmother Hypothesis and concludes, correctly, that the effect on ancient hunter-gather societies could not possibly have been significant enough to be adaptive.

The same reasoning applies to the "Mother Hypothesis," which claims that by going through menopause a mother will avoid the risks of future childbirths enabling her to concentrate on raising her existing children. Both of these hypotheses assume that "just saying no" was not a reasonable strategy in ancient societies and that's why menopause was necessary.

So what's the alternative if you are committed to an adaptive just-so story? You are going to be shocked ... menopause evolved to benefit daughters-in-law!!! (Our daughter-in-law will be so pleased.)

I'm not even going to dignify such a stupid idea by pointing out the obvious flaws.

In case you haven't clued in by now, the bottom line is that all these hypotheses are flawed from the get-go because they all make the unnecessary assumption that the pain and suffering of menopause are adaptive. What if they aren't? What if menopause is neutral with respect to evolution or even maladaptive? What's the point of making up irrational just-so stories when there's no evidence to suggest that menopause has any positive effect of fitness?


Get a Job

 
Assistant Professor, Tenure Stream
Dept. of Cell & Systems Biology
University of Toronto


The Department of Cell & Systems Biology at the University of Toronto invites applications for a tenure track faculty position to be appointed at the Assistant Professor level in the field of Systems Biology to begin July 1, 2009.

We particularly encourage applications from candidates who have demonstrated excellence in addressing fundamental questions in biology using high-throughput approaches or gene/protein network analyses with bioinformatic, genomic, proteomic, or imaging tools. Our vision is to advance systems biology-based research, with a specific interests in developing expertise in systems neurobiology, but we welcome applicants from all others areas of systems biology which complement existing strengths in the department (www.csb.utoronto.ca).

Candidates should have at least two years of research experience beyond their doctoral degree. In addition to pursuing a vigorous, internationally-recognized research program, the successful candidate will contribute to undergraduate and graduate teaching in the molecular life sciences. The successful candidate would also be expected to network with researchers university-wide to take advantage of the extensive resources in systems biology at the University of Toronto and its affiliated institutions. A generous start-up package will be provided. Salary will be commensurate with qualifications and experience.

We encourage qualified applicants to submit their applications online at: www.jobs.utoronto.ca/faculty.htm. Applicants should submit their curriculum vitae, copies of significant publications, and statements of research and teaching interests. Applicants should also arrange for three confidential letters of recommendation to be sent directly to: Professor Daphne Goring, Chair, Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada; or by email to search@csb.utoronto.ca by January 31, 2009.

The University of Toronto offers the opportunity to teach, conduct research and live in one of the most diverse cities in the world, and is responsive to the needs of dual career couples. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.



Poinsettias Are Poisonous

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.
Dr. Vreeman and Dr. Carroll found that the largest study of poinsettia "toxicity" to date involved an analysis of 849,575 plant exposures reported to the American Association of Poison Control Centers. None of the 22,793 poinsettia cases revealed significant poisoning. No one died from poinsettia exposures or ingestions, and more than 96 percent did not even require treatment in a health care facility. Another study, looking at poinsettia ingestion by rats, could not find a toxic amount of poinsettia, even at doses which would be the human equivalent of consuming 500-600 poinsettia leaves or a pound and a half of the plant's sap. Dr. Vreeman cautions, though, that you should always call a poison control center if someone eats a plant not intended for consumption.



Suicides Increase Over the Holidays

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.
The holidays can bring out the worst in people, and the stresses of family get-togethers, loneliness, and the cold, dark winter months are commonly thought to increase the number of suicides at Yule time. But studies conducted around the globe show that, while the holidays may be a difficult time for some, there is no scientific evidence to suggest a holiday peak in suicides, according to Dr. Vreeman and Dr. Carroll. Furthermore, suicides are actually more common during warm and sunny times of the year.



Sugar Makes Kids Hyperactive

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.
This is without a doubt false, report Dr. Vreeman and Dr. Carroll, who are both pediatricians at Riley Hospital for Children. They write that "in at least 12 double-blinded, randomized, controlled trials, scientists have examined how children react to diets containing different levels of sugar. None of these studies, not even studies looking specifically at children with attention deficit-hyperactivity disorder, could detect any differences in behavior between the children who had sugar and those who did not." This includes sugar from candy, chocolate and natural sources. Even in studies of children who were considered "sensitive" to sugar, children did not behave differently after eating sugar-full or sugar-free diets.



Thursday, December 18, 2008

Let's Count the Ways a Creationist Can Go Wrong

 
The latest posting on Uncommon Descent tries to undermine the concept of a natural origin of life [Life From Chiral Crystals . . . Really?]. Maybe one of these days they'll actually put up some evidence to support Intelligent Design Creationism instead of always attacking science.1

Patrick is worried about the chirality problem, which can be pretty well explained by just applying a bit of common sense [Amino Acids and the Racemization "Problem"]. Unfortunately, it's not just the IDiots who are confused about the chirality problem. Many chemists and biologist also seem to have weird ideas about the requirement for 20 L-amino acids when life began.

Patrick quotes Timothy Standish who says,
Much as the Miller-Urey experiment demonstrated that it is possible to produce insignificant yields of a very few biologically important monomers in a laboratory device, Noorduin et al. demonstrated that chemists are capable of producing enantiomerically pure crystals under laboratory conditions. This laboratory technique fails to show a mechanism by which enatiomerically pure solutions of all 20 amino acids used in protein construction may have existed before the advent of life, not to mention the other chiral molecules found in living things. As a consequence, the chirality problem for chemical evolution remains unresolved by this technique.
How many things are wrong with this paragraph?


1. Not holding my breath.

Speciation in Monkeyflowers

 
Within a species there may be distinctive subspecies that have different allele frequencies. The differences are maintained because there is restricted gene (allele) flow between them. The two subspecies may look very different or they may be very similar in appearance.

Genetic exchange between the subspecies is often prevented because the subspecies are geographically separated. This is the first step on the path to allopatric speciation. But genetic exchange can also be restricted by other mechanisms, for example the timing of reproduction, that occurs even if the subspecies inhabit the same environment. This could lead to sympatric speciation.

In either case, the two subspecies will become distinct species—as defined by the biological species concept—when it becomes impossible to form hybrids due to genetic incompatibility. The study of actual speciation events is a hot topic in evolution these days. One of the goals is to identify the genes responsible for preventing the formation of fertile hybrids. The other goal is to identify the mechanism by which the alleles of these genes become fixed in the subspecies. Is it by natural selection or random genetic drift? (Shuker et al. 2005)

One of the best studied examples of speciation in action is due to the work of H.D. Bradshaw and Douglas Schemske at the University of Washington in Seattle, Washington (USA) (Schemske is now at Michigan State University). They studied two species of monkeyflowers that grow near streams and rivers in the mountains and valleys of western North America.

Mimulus lewisii (top) is found primarily at higher elevations (1600 m to 3000 m) while Mimulus cardinalis (right) grows at lower elevations (sea level to 2000 m). Their ranges overlap at moderate elevations in the mountains of California but hybrids are exceedingly rare.

The species differ in a number of characteristics including leaf shape and stem height but the most obvious differences are in the flowers. Mimulus lewsii has pink flowers that are quite open. They attract bumblebees and in the wild 100% of pollinations within this subspecies are by bees. Mimulus cardinalis has red flowers with a more narrow shape. These flowers attract hummingbirds who are responsible for 98% of pollination events in M. cardinalis.

When crossed in a greenhouse, the two species produce fertile hybrids so technically they are not really species but subspecies.

Ramsey et al. (2003) have studied the barriers to gene flow in the wild. Much of it is due to ecogeographic isolation, which is a fancy way of saying that the species don't often come in contact. They grow at different elevations and each species has become adapted to that elevation so that M. lewisii, for example, does not survive well at low elevations and M. cardinalis can't take the cold and the shorter growing season at high elevations.

The fact that the two species have different pollinators is a major factor in preventing gene flow between them. Hummingbirds hardly ever visit M. lewisii and in the overlapping zones there were very few recorded instances of bees visiting flowers from both species. Thus, the opportunities for cross-pollination were effectively zero. What this means is that, "even in sympatry these species are isolated to a large degree by pollinators" (Ramsey et al. 2003).

There are other factors contributing to genetic isolation. The hybrid plants are somewhat less fit and cross-pollination results in fewer seeds than pollination within a (sub)species. The sum of all these factors means that, in the wild, the total reproductive isolation between the two species is 0.9974 to 0.9998. In other words, they don't mix! (But recall that they can readily form fertile hybrids when crossed in the greenhouse.)

In this example, a major component of the restricted gene flow is due to physical separation of the species and that separation is the result of adaptation to different environments. In that sense, the path to speciation is driven, in part, by natural selection. The species are not genetically incompatible so we're not dealing with mutations that prevent hybridization as would be the case if they were true biological species.

Attention has focused on flower color and shape since that determines whether an individual is pollinated by bumblebees or hummingbirds. It's another step toward preventing gene flow between the species. Is it due primarily to selection or drift?

Schemske and Bradshaw (1999) identified a locus, called yellow upper (YUP), that plays a large role in determining flower color in the two species. The locus affects carotenoid distribution in the petals. In M. cardinalis carotenoids are found throughout the petals and the flowers are red. Bees are not attracted to red flowers. The YUP allele in M. lewisii results in less carotenoid and the flowers are pink. These flowers attract bees.

A subsequent study by Bradshaw and Schemske (2003) established that the YUP alleles are directly responsible for much of the pollinator discrimination observed in monkeyflowers. In the second study the authors created near-isogenic lines (NIL) that differed only at the YUP locus.

The normal M. lewisii flower is pink and the petals are in an open shape (a). The normal M. cardinalis flower is red and the shape of the flower is quite different (c). The dominant YUP allele from M. lewisii prevents carotenoid deposition and when it is bred into M. cardialis the flowers are pink (d). The recessive yup allele from M. cardinalis causes more carotenoid to be deposited making the flowers orange in an M. lewisii background (b).

The plants were tested in a natural environment where the ranges of the two species overlapped and both bees and humingbirds were common. Bees preferred the pink flowers whether they were in an M. lewisii background or an M. cardialis background. Conversely, hummingbirds preferred the orange and red flowers in both backgrounds. Thus, the two species have adapted to different pollinators and a large part of this adaptation is due to flower color.

Here's where it gets tricky. Is the switch from bee pollination to hummingbird pollination driven by natural selection? In other words, when the mutation causing red flowers first arose did it confer a fitness advantage on the individuals that came to be pollinated by hummingbirds?

Here's how Bradshaw and Schemske (2003) address this question,
As ‘mutations’ at the YUP locus decrease visitation by the current pollinator guild, and simultaneously increase visitation by a new pollinator guild, are there plausible ecological circumstances in which the mutant might be favoured by natural selection? The combined rate of bumblebee and hummingbird visitation to the yellow-orange-flowered ‘mutants’ of M. lewisii is just 26% of that to the wild-type pink flowers, and the combined rate for dark-pinkflowered ‘mutants’ of M. cardinalis is 95% of the wild type. This implies that a change in the relative abundance of bumblebees and hummingbirds, compared with the pollinator assemblage present during our field experiments, would be required for the mutant to be favoured by natural selection in the common ancestor of M. lewisii and M. cardinalis. The change in relative abundance of pollinators necessary to produce equal visitation to both flower colour phenotypes can be estimated from our data. A ninefold decrease in the relative abundance of bumblebees would produce equal combined visitation rates in the wild-type pink-flowered and ‘mutant’ yellow-orange-flowered M. lewisii NILs. At the equilibrium point, 99% of visitors to wild-type M. lewisii flowers would be bumblebees, whereas 87% of visitors to ‘mutants’ would be hummingbirds. In the M. cardinalis NILs, a twofold increase in the relative abundance of bumblebees would produce equal visitation rates to pink and red flowers. At the equilibrium point, hummingbirds would be virtually the only visitor to the wild-type red M. cardinalis flowers, and remain the major visitor (89% of visits) even to the dark-pink ‘mutants.’
In order for the red flower allele to be fixed by natural selection there would have to be a significant decline in the bee population at the time the mutation arose. Presumably, this decline would have only occurred in a small part of the range leading to a subpopulation with red flowers while the main, wild-type, population (pink flowers) continued to be visited by bees.

The authors don't mention the other possibility; namely, that the red flower allele (yup) spread in a subpopulation by random genetic drift. In this scenario, there is no selective advantage to individual plants if they are pollinated by humingbirds. Clearly the evolution of pollinator discrimination by flower color will lead to restricted gene flow between the two species but it is not clear whether this epiphenomenon is due to selection for hummingbird pollination or random genetic drift.


[Photo Credits: Mimulus lewisii or Purple monkey-flower (top) is from flickr. Mimulus cardinalis or Cardinal monkeyflower (second from top) is from the Arizona-Sonore Desert Museum.


Bradshaw, H.D. Jr. and Schemske, D.W. (1999) Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature 426:176-178. [doi:10.1038/nature02106] [PDF]

Ramsey, J., Bradshaw, H.D. Jr., Schemske, D.W. (2003) Components of Reproductive Isolation between the Monkeyflowers Mimulus lewisii and M. cardinali (Phrymaceae). Evolution 57:1520-1534. [PDF]

Schemske, D.W. and Bradshaw, H.D. Jr. (2003) Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proc. Natl. Acad. Sci. (USA) 96:11910-11915. PDF]

Shuker, D.M., Underwood, K., King, T.M., and Butlin, R.K. (2005) Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection. Proc. Biol. Sci. 272:2491-2497. [DOI: 10.1098/rspb.2005.3242]

Is Bill O’Reilly Really this Stupid?

 
Don't answer that. It's a rhetorical question.

Honestly, I just don't understand how someone who's a prominent television personality can be so totally ignorant of the very issue that he rants about. It's not rocket science. The law isn't that hard to understand.

Maybe there's something about being religious that clouds the mind?

Listen for the following words from attorney Megan Kelley, "I've never met a non-lawyer who argues the law so confidently, albeit, so wrongly."




[Hat Tip: Friendly Atheist: You Are Wrong! You Are *So* Wrong!]