Like John Wilkins, I too have visited Italy.
John Wilkins of Evolving Thoughts is currently in Venice, Italy. He has just visited the Basilica San Marco (St. Mark's Basilica) according to What I am doing on my holidays….This is interesting, I think, in the context of Gould’s and Lewontin’s paper. It shows that claims of things being adaptive or not depend crucially on what one counts as the “task” of a structure. Since I think that everything is subjected to selection pressure at all times (sometimes not enough to overcome the noise of statistical properties), counting what is, and what isn’t, adaptive is a bit of a personal call, in the absence of access to the historical processes of particular traits. I am becoming more of an adaptationist these days.The idea that many alleles might be slightly beneficial or slightly detrimental isn't very controversial. But that's not what John is saying. As I understand him, he's saying there can be no such thing as a truly neutral allele. He seems to be saying that anyone who believes otherwise is making a "personal call." A personal call that he believes is wrong since he thinks (i.e. his personal call) that everything is subject to natural selection.
One of the papers I liked was Seven Types of Adaptationism by Tim Lewens (Lewens, 2009). The seven types are:A Empirical adaptationismsThere are problems with all seven forms of adaptationism but the nice thing about Lewens' paper is that he effectively refutes #4, #5, and #7. In the case of methodological adaptationism it's just not true that the default assumption has to be adaptation. Evolutionary biology will be just as productive in the long run if drift is the default assumption and adaptation has to be proven.
1. Pan-selectionism–natural selection is the most significant of the evolutionary forces that act on populations.
2. Good-designism–evolutionary processes tend to result in organisms with suites of well-designed traits. Most lineages are highly evolvable.
3. Gradualism–adaptation is always the result of selection acting on gradual
variation.
B Methodological Adaptationisms
4. Weak heuristic adaptationism–those traits that are adaptations are likely to be correctly recognised as such only if we begin by assuming that all traits are adaptations.
5. Strong heuristic adaptationism–only by beginning to think of traits as adaptations can we uncover their true status, whether they are adaptations or not.
C Disciplinary Adaptationism
6. Explanatory adaptationism–an evolutionary biologist’s proper business is the study of adaptations.
D Epistemological Adaptationism
7. Epistemological optimism–investigators have access to the data that reliably discriminate between conflicting evolutionary hypotheses.
Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205:581-598.
Lewens, T. (2009) Seven types of adaptionism. Biol. Philos. 24:161–182. [doi: 10.1007/s10539-008-9145-7]
This is the earliest posting of a Monday's Molecule. It should make the contest open to a whole new category of Sandwalk readers, especially those in Europe who will see it long before the readers in North America are awake. 
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The first person to identify the molecule and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.The two kinds people who believe that religion and evolution can not coexist are extreme atheists and extreme religious fundamentalists. Everyone else doesn't really have a problem. [A majority] of Americans believe that a belief in god is compatible with evolution.Many atheists interpret this kind of statement as an insult and Jerry Coyne called it "an anti-atheist crack." This prompted Joshua Rosenau to respond like this.
First, note that Kevin Padian is a fairly open atheist, so if this line were "anti-atheist" it would have to be a sort of self-hating atheism. Second, how is it factually wrong? Some atheists (but not all) think science and religion are incompatible. Some religious fundamentalists also think this. There are also a bunch of people in the middle of the spectrum of belief who do not think that. Whether these represent a majority of Americans depends how you ask the question and what you do with undecided responses, but it is absolutely the case that most Americans belong to religious groups whose governing bodies have asserted the compatibility of science (including evolution) and their brand of religion.Yes, Josh, there's a reason why some atheists are annoyed at remarks like that. Here's a list ....
What, then, makes Padian's factually correct statement about the beliefs of some atheists a "crack"? Is there any method at all to Coyne's outrage
1. What are those areas? I wonder if Josh or Kevin has a list?
One of the popular techniques in psychology these days is to analyze brain activity in an MRI machine. In a typical experiment, the subject will be shown various images and the machine will maps those parts of the brain that are responding.Subject. One mature Atlantic Salmon (Salmo salar) participated in the fMRI study. The salmon was approximately 18 inches long, weighed 3.8 lbs, and was not alive at the time of scanning.The point of the study was to show that you need to be aware of false positives and make the effort to filter the data in order to remove them.
Task. The task administered to the salmon involved completing an open-ended mentalizing task. The salmon was shown a series of photographs depicting human individuals in social situations with a specified emotional valence. The salmon was asked to determine what emotion the individual in the photo must have been experiencing.
Design. Stimuli were presented in a block design with each photo presented for 10 seconds followed by 12 seconds of rest. A total of 15 photos were displayed. Total scan time was 5.5 minutes.
Preprocessing. Image processing was completed using SPM2. Preprocessing steps for the functional imaging data included a 6-parameter rigid-body affine realignment of the fMRI timeseries, coregistration of the data to a T1-weighted anatomical image, and 8 mm full-width at half-maximum (FWHM) Gaussian smoothing.
Analysis. Voxelwise statistics on the salmon data were calculated through an ordinary least-squares estimation of the general linear model (GLM). Predictors of the hemodynamic response were modeled by a boxcar function convolved with a canonical hemodynamic response. A temporal high pass filter of 128 seconds was include to account for low frequency drift. No autocorrelation correction was applied.
Voxel Selection. Two methods were used for the correction of multiple comparisons in the fMRI results. The first method controlled the overall false discovery rate (FDR) and was based on a method defined by Benjamini and Hochberg (1995). The second method controlled the overall familywise error rate (FWER) through the use of Gaussian random field theory. This was done using algorithms originally devised by Friston et al. (1994).
[Hat Tip: John Hawks]
An even smaller percentage will actually admit to being an atheist or an agnostic in spite of the fact that their answers to other questions identify them as atheists or agnostics. The "belonging" category refers to the answer to the question, "What is your religion, if any?" It's a way of allowing respondants to self-identify as atheists or agnostics. [Hat Tip: Razib Khan]
It's a well-known fact that the average intelligence of university students has been declining over the past four or five decades. This is true in spite of the fact that the average university grades have been going up.1. This is not an argument against increasing the participation rate and expanding university enrolment. I'm in favor of that. Let's just realize that there are consequences that universities need to deal with.
The real question we need to address is gradation rate. In an ideal world, what percentage of those who enter university should graduate? Should it be 100%? 50%?
The data, referred to as "the Canadian problem" by some scientists outside this country, are reported to link getting a flu shot last year with double the risk of contracting swine flu this year.Say what?
The link, if real, is to mild disease. One person who has seen the study says it seems to suggest that those who got a seasonal flu shot were less likely to develop severe disease if they became infected than those who hadn't received the shot.
Drawn from a series of studies from British Columbia, Quebec and Ontario, the work is led by Dr. Danuta Skowronski of the British Columbia Centre for Disease Control and Dr. Gaston De Serres of Laval University.This is unethical behavior at many levels. First, journals have no right to block access to essential information that's needed to make public health decisions in the middle of a pandemic. That journal should be identified and forced to defend it's policy. Second, no reputable scientists should agree to such an embargo in the first place. Third, if the journal and the scientists enter into a deal to remain silent then how come we know about this study? It sounds like the authors may want to have their cake and eat it too.
They have submitted the paper to an unnamed scientific journal and are therefore constrained about what they can say about the work. Journals bar would-be authors from discussing their results before they are published.
"For me, it's very important that we respect the peer-review process as good scientists. Because the implications ... are important," Skowronski said in an interview Wednesday.
"And if there are methodologic flaws, we need to be assured that every stone was turned over to make sure what we're reporting is valid."
The last issue of SEED magazine was published in June. Since then, I've been scanning the shelves of my local convenience stores looking for the latest informative article by PZ Myers and the latest fuel for complaints about the quality of science journalism.We are currently finishing an exciting redesign that will be on press this fall. This will also be our first issue with the new tagline.This sounds ominous. Is the print version of SEED dead?
It's not surprising to discover that creationists are opposed to the idea that life began by purely natural processes. After all, that's at the heart of the dispute between creationists and scientists. Accidental origin of life is the basic thesis of origin of life researchers. Life all just somehow sort of happened one day, billions of years ago, under the right conditions – which we may be able to recreate. But there is a constant, ongoing dispute about just what those conditions were.You can win a creationist book for the best response to her question.
Here is the problem I have always had with accidental origin of life: It amounts to spontaneous generation. However, banishing the doctrine of spontaneous generation played a key role in modern medicine’s success. If we assume that life forms (for medical purposes, we focus on pathogens) cannot start spontaneously, then they must have been introduced. Hence, we can develop procedures for a sterile operating room or lab.
If life can be spontaneously generated, why isn’t it happening now? Conditions for life today are probably as good as they have ever been, and maybe better. For over 500 million years they have obviously been good for complex life forms, and for billions of years they have been good for simple ones.
The accidental origin of life idea hurts science because it militates against the vital principle of causation, the rational and indispensible standard on which science is based. The first question any researcher asks is this: “How did it happen? or—What caused it? Yet, the concept of spontaneous generation popularizes the idea that physical events can occur without causes—that there need not be a “how”—that they can “just happen.”Are there any evolutionists out there who believe that the first living cell just "poofed" into existence without any cause or antecedents? If you believe this then please post a comment below.
Consider the following proposition: Streets don’t just “get wet.” Using the scientific and philosophical principle of causation, we understand that something had to cause the streets to get wet. So, we say that if the streets are wet, then it must be raining, or else someone turned on a fire hydrant, or we look for some other reason. But if, as Darwinists or postmodern cosmologists claim, physical events do not always need causes or necessary conditions, that is, if something really can come from nothing, then streets can indeed just get wet. With this mind set, science is severely compromised. If, indeed, something can appear spontaneously or without a cause, why cannot it happen again somewhere else in some other situation?
In keeping with that point, if one thing can “just happen,” then why cannot anything just happen? Why not everything? Under these circumstances, how could the scientist know which things were caused and which ones were not? Science would become an intellectual madhouse where the impossible is affirmed with confidence and the obvious is dismissed with disdain, which, come to think of it, is not a bad description of Darwinst epistemology. For Darwinists, and for postmodern cosmologists, a universe can pop into existence, life can come from non-life, and, yes, streets could, in principle, just “get wet.” Science cannot survive this irrational mind set indefinitely.
[Hat Tip: ScienceRoll]
"in recognition of his work on the physiology of digestion, through which knowledge on vital aspects of the subject has been transformed and enlarged"
Ivan Petrovich Pavlov (1849 - 1936) (Иван Петрович Павлов) won the Noble Prize in 1904 for his contribution to understanding the physiology and biochemistry of digestion. Part of his contribution was the discovery that some of the digestion enzymes needed to be activated before they could work in the stomach [Monday's Molecule #133].
The knowledge gained from his studies on digestion had no practical application in medicine. They simply advanced our understanding of how our bodies work. In presenting the Nobel Prize the presenter, Count K.A.H. Mörner, took pains to make this point clear and to pronounce it a good thing. Science for the sake of knowledge. In the early days opinions on the course of digestion were speculations as to what was termed as «cooking» or «grinding» in the stomach etc. So long as the digestive processes could not be observed or investigated directly in the stomach no real knowledge could be obtained. An accident turned physiological research in this field in a direction which has later become very important. In the 1820's a young man sustained a gunshot wound in the stomach and developed a gastric fistula which to some extent permitted the gastric processes to be studied. Observations were carried out on this man by the American physician W. Beaumont. This accidental path of investigation, allowing actual observation of processes taking place in the digestive tract, was later followed by many workers using animals. Technique is an important factor in such experiments and has been perfected in a masterly way by Pavlov, whose animals remain in good health, without any injury to the function of their digestive tract, permitting observation and systematic investigation over an almost unlimited period.
These methods for the study of the physiology of digestion established by Pavlov have been taken up by various physiological institutions, but above all much important work was performed in his own laboratory. From this has followed a far-reaching transformation of our knowledge in this field which has also been enriched by new fundamental facts.
The following may be mentioned as an illustration.
The digestive canal can be influenced in various ways by the nervous system. When we remember that the nervous system can induce not only the secretory processes as well as the movements of various parts of the system, but also can bring such processes to a standstill, that it controls the blood supply to these organs and that sensory nerves arise from them, we can get an idea of the complexity one encounters. The complications become still greater when it is realised that we must take into account not only nervous pathways having their origin in the brain or the spinal cord, but also the sympathetic nervous system, and that we have further to pay attention to the interdependence between the different parts of the digestive system through the nerves, so that variations in the behaviour of one may affect that in other organs.
It is in the nature of things that cognition of the scope and character of the functional interdependence of the nervous system and the digestive organs is of great importance to the knowledge of the physiology of these organs. It is also clear that one can only hope that answers to these complicated questions will advance step by step by much research. In this respect Pavlov has acquired very great merit. He has revealed new points of view and has fruitfully stimulated the solution of these problems, and through his methods has made it possible to reach conclusive analysis of them.
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
[Photo Credit: Pasteur [Hulton Archive/Getty Images]
Today's "molecule" is actually several molecules, one of which is shown in a diagram below the electron micrograph. You have enough clues to identify this virus. As soon as you get the right answer it will lead you directly to one or more Nobel Laureates.
