Wednesday, December 11, 2013

Randy Wayne Schekman (born December 30, 1948) is an American cell biologist at the University of California, Berkeley,[6] and former editor-in-chief of Proceedings of the National Academy of Sciences.[2][7][8] In 2011 he was announced as the editor of eLife, a new high profile open access journal published by the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust launching in 2012.[9] He was elected to the National Academy of Sciences in 1992.[10] Schekman shared the 2013 Nobel Prize for Physiology or Medicine with James Rothman and Thomas C. Südhof.[5][11]


Funders and universities, too, have a role to play. They must tell the committees that decide on grants and positions not to judge papers by where they are published. It is the quality of the science, not the journal's brand, that matters. Most importantly of all, we scientists need to take action. Like many successful researchers, I have published in the big brands, including the papers that won me the Nobel prize for medicine, which I will be honoured to collect tomorrow.. But no longer. I have now committed my lab to avoiding luxury journals, and I encourage others to do likewise.

Monday, October 28, 2013

Problems with scientific research
How science goes wrong

Oct 19th 2013 |From the print edition

[[There are a lot of articles with this subject, but due to the deserved reputation of the Economist I am putting this one on the blog. D. G.]]
In this section
·                                 How science goes wrong
What a load of rubbish
If it’s broke, fix it

Sunday, October 6, 2013

Evolution, Speeded by Computation

‘Probably Approximately Correct’ Explores Nature’s Algorithms

  • SAVE
  • E-MAIL
Our daily lives are growing ever more dependent on algorithms, those omnipresent computational procedures that run programs on our laptops, our smartphones, our GPS devices and much else. Algorithms influence our decisions, too: when we choose a movie on Netflix or a book on Amazon, we are presented with recommendations churned out by sophisticated algorithms that take into account our past choices and those of other users determined (by still other algorithms) to be similar to us.

The importance of these algorithms in the modern world is common knowledge, of course. But in his insightful new book “Probably Approximately Correct,” the Harvard computer scientist Leslie Valiant goes much further: computation, he says, is and has always been “the dominating force on earth within all its life forms.” Nature speaks in algorithms.
Dr. Valiant believes that phenomena like evolution, adaptation and learning are best understood in terms of “ecorithms,” a term he has coined for algorithms that interact with and benefit from their environment. Ecorithms are at play when children learn how to distinguish cats from dogs, when we navigate our way in a new city — but more than that, Dr. Valiant writes, when organisms evolve and when brain circuits are created and maintained.
Here is one way he illustrates this complex idea. Suppose we want to distinguish between two types of flowers by measuring their petals. For each petal we have two numbers, x for length and y for width. The task is to find a way to tell which type of flower a petal with given measurements x and y belongs to.
To achieve this, the algorithm is fed a set of examples meant to “train” it to come up with a good criterion for distinguishing the two flowers. The algorithm does not know the criterion in advance; it must “learn” it using the data that are fed to it.
So it starts with a hypothesis and tests it on the first example. (Say flower No. 1’s petals can be described by the formula 2x—3y>2, while for Flower No. 2 it’s 2x—3y<2 .="" a="" algorithm="" along.="" an="" and="" applied="" as="" by="" certain="" example.="" example="" goes="" hypothesis="" if="" is="" it="" learning="" literally="" misclassifies="" new="" next="" p="" precise="" proceed="" rule="" that="" the="" to="" updated="" we="" works="">
A striking mathematical theorem is that if a rule separating the two flowers exists (within the class of criteria we are considering, such as linear inequalities), then our algorithm will find it after a finite number of steps, no matter what the starting hypothesis was.
And Dr. Valiant argues that similar mechanisms are at work in nature. An organism can adapt to a new environment by starting with a hypothesis about the environment, then testing it against new data and, based on the feedback, gradually improving the hypothesis by using an ecorithm, to behave more effectively.
“Probably Approximately Correct,” Dr. Valiant’s winsome title, is his quantitative framework for understanding how these ecorithms work. In nature, there is nothing so neat as our idealized flower algorithm; we cannot really hope to get a precise rule distinguishing between two types of flowers, but can hope only to have one that gives an approximate result with high probability.
[[Shades of Thomas Nagel!! - D.G.]]
This is an ambitious proposal, sure to ignite controversy. But what I find so appealing about this discussion, and the book in general, is that Dr. Valiant fearlessly goes to the heart of the “BIG” questions. (I don’t know him, though we share an editor at Basic Books.) He passionately argues his case, but is also first to point out the parts of his theory that are incomplete, eager to anticipate and confront possible counterarguments. This is science at its best, driven not by dogma and blind belief, but by the desire to understand, intellectual integrity and reliance on facts.
Many other topics are discussed, from computational complexity to intelligence (artificial and not), and even an algorithmic perspective on teaching. The
book is written in a lively, accessible style and is surprisingly entertaining. It’s funny how your perception of even mundane tasks can change after reading it — you start thinking algorithmically, confirming Dr. Valiant’s maxim that computer science is “more about humans than about computers.”
Edward Frenkel, a professor of mathematics at the University of California, Berkeley, is the author of the new book “Love and Math.”

Sunday, August 11, 2013

Current Limits of Science -a few of very many.

About six months ago I had a tragi-comic exchange with the principal of a North American day school. One of his students, sixteen years old, challenged his teacher and the rest of the class with the words: "Since science can explain everything, there is no need to believe in G-d." I suppose one should both laugh and cry: laugh at the colossal ignorance of the student, and cry for the damage done by the false impression of the scope of science. Just in case that student is not alone, here is a [very partial] list of some outstanding mysteries for which science has no clue. [I invite readers t write to me with more that I can add.]

1. Dark matter
In astronomy and cosmologydark matter is a type of matter hypothesized to account for a large part of the total mass in theuniverse. Dark matter cannot be seen directly with telescopes; evidently it neither emits nor absorbs light or other electromagnetic radiation at any significant level.[1] Instead, its existence and properties are inferred from its gravitational effects on visible matter, radiation, and the large-scale structure of the universe. According to the Planck mission team, and based on the standard model of cosmology, the total mass–energy of the universe contains 4.9% ordinary matter, 26.8% dark matter and 68.3% dark energy.[2][3]Thus, dark matter is estimated to constitute 84.5% of the total matter in the universe and 26.8% of the total content of the universe.[4].................According to consensus among cosmologists, dark matter is composed primarily of a not yet characterized type of subatomic particle.[6][7] The search for this particle, by a variety of means, is one of the major efforts in particle physics today.[8]

2. Dark energy.
In physical cosmology and astronomydark energy is a hypothetical form of energy that permeates all of space and tends toaccelerate the expansion of the universe.[1] Dark energy is the most accepted hypothesis to explain observations since the 1990s that indicate that the universe is expanding at an accelerating rate. According to the Planck mission team, and based on the standard model of cosmology, the total mass–energy of the universe contains 4.9% ordinary matter, 26.8% dark matter and 68.3% dark energy.[2][3][4]
Two proposed forms for dark energy are the cosmological constant, a constant energy density filling space homogeneously,[5] andscalar fields such as quintessence or modulidynamic quantities whose energy density can vary in time and space. [[In other words, two contradictory proposals mean that we do not understand what it is.]]

[[Taking 1 and 2 together, all our science explains at most 4.9% of the total mass of the universe. And by the way, not all is well with the 4.9% either  Where are the Missing Baryons?
Credit: Spectrum: NASA/CXC/Univ. of California Irvine/T. Fang Illustration: CXC/M. WeissDark energy and dark matter combine to occupy approximately 95 percent of the universe, with regular matter making up the remaining 5 percent. But, researchers have been puzzled to find that more than half of this regular matter is missing. 

This missing matter is called baryonic matter, and it is composed of particles such as protons and electrons that make up majority of the mass of the universe's visible matter.

Some astrophysicists suspect that missing baryonic matter may be found between galaxies, in material known as warm-hot intergalactic medium, but the universe's missing baryons remain a hotly debated topic.]]

3.  See the posts on this blog undr the label "evolution" for the many failures of that theory.

Explanatory gap

From Wikipedia, the free encyclopedia
To take an example of a phenomenon in which there is no gap, imagine a modern computer: as marvelous as these devices are, their behavior can be fully explained by their circuitry, and vice versa. By contrast, it is thought by many mind-body dualists (e.g. René DescartesDavid Chalmers) that subjective conscious experience constitutes a separate effect that demands another cause, a cause that is either outside the physical world (dualism) or due to an as yet unknown physical phenomenon (see for instance Quantum mind,Indirect realism).
Proponents of dualism claim that the mind is substantially and qualitatively different from the brain and that the existence of something metaphysically extra-physical is required to 'fill the gap'.
Others, such as Joseph Levine, have wished to either remain silent on the matter or argue that no such metaphysical conclusion should be drawn.[1] He agrees that conceivability (as used in the Zombie and inverted spectrum arguments) is flawed as a means of establishing metaphysical realities; but he points out that even if we come to the metaphysicalconclusion that qualia are physical, they still present an explanatory problem.
Many philosophers consider experience to be the essence of consciousness, and believe that experience can only fully be known from the inside, subjectively. But if consciousness is subjective and not visible from the outside, why do the vast majority of people believe that other people are conscious, but rocks and trees are not?[41] This is called the problem of other minds.[42] It is particularly acute for people who believe in the possibility of philosophical zombies, that is, people who think it is possible in principle to have an entity that is physically indistinguishable from a human being and behaves like a human being in every way but nevertheless lacks consciousness.[43]

Mind–body problem[edit source | editbeta]


[[This list of alternative theories shows how  far we are from an understanding of consciousness.]]

4. The origin of life. [Not to be confused with the theory of evolution which tries to explain only how life develops, not how it originated.] 
For a very thorough review of the decade of scientific despaif dealing iwth this problem, look here

And look at this summary of the various proposals

  • 3 Current models
  • 4 Other models

  • The Scientific American February 2013 contains the following iconoclastic articles:

  • 5. Europe's winter weather

  • New Simulations Question the Gulf Stream’s Role in Tempering Europe’s Winters


    6. How does the brain store memory? 

    A Single Brain Cell Stores a Single Concept [Preview]

    7. What causes aging? 

    Gems genetically engineered the roundworms so they no longer produced certain enzymes that act as naturally occurring antioxidants by deactivating free radicals. Sure enough, in the absence of the antioxidants, levels of free radicals in the worms skyrocketed and triggered potentially damaging oxidative reactions throughout the worms' bodies. [[But they did not die any faster than normal worms. The whole understanding of he process of aging is now in doubt. ]]
    8. Human origins. 


    By Katherine Harmon 


    end of articles from the Scientific American.