Archive for April, 2013

Random and Undirected

April 29, 2013

The Origin of Species is essentially about eliminating the need to invoke God to explain life. And Charles Darwin made no bones about it. In a letter to his mentor, the geologist Charles Lyell on 11th October 1859, Darwin wrote,

But I entirely reject as in my judgment quite unnecessary any subsequent addition “of new powers, & attributes & forces”; or of any “principle of improvement”… If I were convinced that I required such additions to the theory of natural selection, I would reject it as rubbish. I would give absolutely nothing for the theory of Natural Selection, if it requires miraculous additions at any one stage of descent.[1]

This has consistently been the position of Darwin’s heirs and the vast majority of evolutionary biologists. Ernst Mayr, widely considered to be one of the most important and influential biologists of the twentieth century, wrote:

The Darwinian revolution was not merely the replacement of one scientific theory by another, but rather the replacement of a worldview, in which the supernatural was accepted as a normal and relevant explanatory principle, by a new worldview in which there was no room for supernatural forces.[2]

 Julian Huxley was the grandson of Darwin’s Bulldog, Thomas Huxley, and a prominent biologist in his own right. He wrote:

Darwinism removed the whole idea of God as the Creator of organisms from the sphere of rational discussion. Darwin pointed out that no supernatural designer was needed; since natural selection could account for any new form of life, there is no room for a supernatural agency in its evolution.[3]

George Gaylord Simpson, one of the leading palaeontologists of the twentieth century, wrote that “Man is the result of a purposeless and natural process that did not have him in mind.”[4]

In Genesis and Genes, I quoted the late Stephen Jay Gould, one of the most famous scientists and popularisers of science in the latter part of the twentieth century. Gould  frequently discussed the “radical philosophical content of Darwin’s message” and its denial of purpose in the universe:

First, Darwin argues that evolution has no purpose… Second, Darwin maintained that evolution has no direction… Third, Darwin applied a consistent philosophy of materialism to his interpretation of nature. Matter is the ground of all existence; mind, spirit, and God as well, are just words that express the wondrous results of neuronal complexity.[5]

Contemporary biology textbooks are adamant that Darwinian evolution is unguided. A popular college biology textbook by Douglas Futuyma declares that “[B]y coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of the life processes superfluous.”[6]

This is what you will find in Invitation to Biology:

Now the new biology asked us to accept the proposition that, like all other organisms, we too are the products of a random process that, as far as science can show, we are not created for any special purpose or as part of any universal design.[7]

 And Evolution (by Strickberger) has this to say:

The advent of Darwinism posed even greater threats to religion by suggesting that biological relationships, including the origin of humans and of all species, could be explained by natural selection without the intervention of a god… In this scheme a god of design and purpose is not necessary…[8]

 And Evolution (by Barton) explains that evolution involves “random genetic drift,” “random mutation,” “random variation,” “random … individual fitness,” and “random reproduction”.

 In 1997, the National Association of Biology Teachers in the USA removed from its description of the evolution of life an assertion that it was an “unsupervised, impersonal, unpredictable and natural process.” Ninety-nine academics, including over 70 evolutionary biologists, sent a letter of protest to the NABT asserting that evolution indeed is “an impersonal and unsupervised process… The NABT leaves open the possibility that evolution is in fact supervised in a personal manner. This is a prospect that every evolutionary biologist should vigorously and positively deny.”[9]

Evolutionary biologists and authors are often at pains to emphasise this point. University of Chicago evolutionary biologist and author Jerry Coyne makes the point concisely:

But any injection of teleology into evolutionary biology violates precisely the great advance of Darwin’s theory: to explain the appearance of design by a purely materialistic process — no deity required.[10]

And the biochemist Larry Moran of the University of Toronto writes that:

The main mechanisms are natural selection and random genetic drift and those two mechanisms act on populations containing variation. The variation is due to the presence of mutations and mutations arise “randomly” with respect to ultimate purpose or goal.[11]

 This sentiment is often encountered in academic papers:

 Mutation is the central player in the Darwinian theory of evolution – it is the ultimate source of heritable variation, providing the necessary raw material for natural selection. In general, mutation is assumed to create heritable variation that is random and undirected.[12]

Francisco Ayala is a former Roman Catholic priest and world-famous evolutionary biologist [See the post Tactics and Deceit to read more about Ayala]. In a 2007 paper Ayala wrote:

Chance is, nevertheless, an integral part of the evolutionary process. The mutations that yield the hereditary variations available to natural selection arise at random. Mutations are random or chance events because (i) they are rare exceptions to the fidelity of the process of DNA replication and because (ii) there is no way of knowing which gene will mutate in a particular cell or in a particular individual. However, the meaning of “random” that is most significant for understanding the evolutionary process is (iii) that mutations are unoriented with respect to adaptation; they occur independently of whether or not they are beneficial or harmful to the organisms. Some are beneficial, most are not, and only the beneficial ones become incorporated in the organisms through natural selection.[13]

What Professor Ayala means by point (iii) can be economically expressed as follows: the Darwinian process is bereft of foresight. This has direct and obvious bearing on the philosophical content of biological evolution, as Ayala points out:

It was Darwin’s greatest accomplishment to show that the complex organization and functionality of living beings can be explained as the result of a natural process – natural selection – without any need to resort to a Creator or other external agent… The scientific account of these events does not necessitate recourse to a preordained plan, whether imprinted from the beginning [this is sometimes referred to as front-loading – YB] or through successive interventions by an omniscient and almighty Designer. Biological evolution differs from a painting or an artifact in that it is not the outcome of preconceived design.

Ayala’s conclusion is concisely expressed:

This is Darwin’s fundamental discovery, that there is a process that is creative although not conscious. And this is the conceptual revolution that Darwin completed: the idea that the design of living organisms can be accounted for as the result of natural processes governed by natural laws. This is nothing if not a fundamental vision that has forever changed how mankind perceives itself and its place in the universe.

 ***

Notwithstanding the above – and we could go on and on demonstrating that the community of evolutionary biologists, as a whole, conceives of evolution as a non-teleological process – there are those who style themselves theistic evolutionists. This position often results in confusion, as we shall presently see.

In July 2005, Christoph Cardinal Schönborn wrote an op-ed in the New York Times in which he stated that “evolution in the neo-Darwinian sense – an unguided, unplanned process of random variation and natural selection – is not [true].”[14]

Ken Miller, a biologist, textbook-writer and prominent exponent of theistic evolution, responded:

But the Cardinal is wrong in asserting that the neo-Darwinian theory of evolution is inherently atheistic. Neo-Darwinism, he tells us, is an ideology proposing that an “unguided, unplanned process of random variation and natural selection” gave rise to all life on earth, including our own species. To be sure, many evolutionists have made such assertions in their popular writings on the “meaning” on evolutionary theory. But are such assertions truly part of evolution as it is understood by the “mainstream biologists” of which the Cardinal speaks? Not at all… This means that biological evolution, correctly understood, does not make the claim of purposelessness.[15]

Huh? Is Miller serious about “mainstream biologists” believing anything except that evolution is unguided and unplanned? Besides everything we said above, consider the following. In 2005, the Kansas State Board of Education sought to introduce changes to the biology syllabus in order to foster critical thinking among students. This involved allowing teachers to introduce scientific criticisms of evolutionary biology. In response, no fewer than 38 Nobel laureates (!) under the auspices of – wait for it – the Elie Wiesel Foundation for Humanity signed a joint statement to the KSBE informing them that,

… evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.[16]

Perhaps Professor Miller does not consider these Nobel Prize-winners representative of the mainstream. But besides his capacity to ignore the obvious, Miller also contradicts himself. Five editions of Miller’s textbook, Biology, stated that “evolution works without either plan or purpose… Evolution is random and undirected.”[17] In his book Finding Darwin’s God, we find the following:

  • Random, undirected process of mutation had produced the ‘right’ kind of variation for natural selection to act upon (Page 51).
  • A random, undirected process like evolution (Page 102).
  • Blind, random, undirected evolution [could] have produced such an intricate set of structures and organs… (Page 137).
  • The random, undirected processes of mutation and natural selection (Page 145)
  • Evolution is a natural process, and natural processes are undirected (Page 244).

 Both the 1991 and 1994 editions of Miller & Levine’s Biology: The Living Science contain the following passage:

Darwin knew that accepting his theory required believing in philosophical materialism, the conviction that matter is the stuff of all existence and that all mental and spiritual phenomena are its by-products. Darwinian evolution was not only purposeless but also heartless – a process in which the rigors of nature ruthlessly eliminate the unfit. Suddenly, humanity was reduced to just one more species in a world that cared nothing for us. The great human mind was no more than a mass of evolving neurons. Worst of all, there was no divine plan to guide us.[18] [Italics in the original.]

***

The confusion generated by Professor Miller’s apparently-schizophrenic writings is, unfortunately, not limited to the Gentile community. I wrote in Genesis and Genes that,

Evolution is inherently indifferent to religion; deities need not apply. But there will always be those who wish to reconcile the irreconcilable. They want to take the world’s most efficient engine for atheism, slap on a veneer of verses, and recast it as a Torah ideal. The result is about as appetising as frosting on a bar of soap. There cannot be a rapprochement between mutually-exclusive concepts. The attempt to apply a layer of religious respectability to evolution is vacuous.

 See Also: The post Tactics and Deceit

https://torahexplorer.com/2013/01/17/423/

 References:

 [1] Letter from Darwin to Charles Lyell, 11th October 1859. See Darwin Correspondence Database,

http://www.darwinproject.ac.uk/entry-2503.

Retrieved 28th April 2013.

[2] Ernst Mayr, book review of Evolution and God, Nature 248 (March 22, 1974): 285.

[3] Tax, S. and Callender, C. (Eds.), Evolution after Darwin, Issues in Evolution (volume III), The University of Chicago Press, Chicago, USA, page 45, 1960.

[4] George Gaylord Simpson, The Meaning of Evolution, revised edition (New Haven: Yale University Press, 1967), page 345.

[5] Stephen Jay Gould, Ever Since Darwin: Reflections in Natural History, pg. 12–13 (W.W. Norton & Co. 1977).

[6] Douglas J. Futuyma, Evolutionary Biology, 3rd edition, Sinauer Associates, 1998, page 5.

[7] Helena Curtis and N. Sue Barnes, Invitation to Biology, 3rd edition. New York: Worth Publishers, 1981:474-75.

[8] Monroe W. Strickberger, Evolution, 3rd edition. Sudbury: Jones and Bartlett Publishers, 2000:70-71.

[9] The Nature of Nature, Bruce L. Gordon and William A. Dembski, editors. ISI Books, Wilmington, Delaware, 2011, page 41.

[10] See http://whyevolutionistrue.wordpress.com/2009/04/22/truckling-to-the-faithful-a-spoonful-of-jesus-helps-darwin-go-down/.

Retrieved 28th April 2013.

[11] See http://sandwalk.blogspot.co.uk/2012/08/is-unguided-part-of-modern-evolutionary.html.

Retrieved 28th April 2013.

[12] An environmentally induced adaptive (?) insertion event in flax, Yiming Chen, Robin Lowenfeld and Christopher A. Cullis, International Journal of Genetics and Molecular Biology Vol. 1 (3), pages 038-047, June 2009. The paper can be read here: http://www.acadjourn.org/IJGMB/PDF/pdf2009/June/Chen%20et%20al..pdf. Retrieved 11th July 2011.

[13] Francisco J. Ayala, “Darwin’s greatest discovery: Design without designer” Proceedings of the National Academy of Sciences USA, 104 (May 15, 2007): 8567-8573. I saw this in an article by Casey Luskin dated 11th August 2012 on the website Evolution News and Views.

[14] See http://www.millerandlevine.com/km/evol/catholic/schonborn-NYTimes.html.

Retrieved 28th April 2013.

[15] See http://www.millerandlevine.com/km/evol/catholic/op-ed-krm.html.

Retrieved 28th April 2013.

[16] The letter used to be available at:

http://media.ljworld.com/pdf/2005/09/15/nobel_letter.pdf

I was not able to retrieve it.

[17] Kenneth Miller and Joseph Levine, Biology (1st ed., 1991), p. 658; (2nd ed., 1993), p. 658; (3rd ed., 1995), p. 658; (4th ed., 1998), p. 658; (5th ed. 2000), p. 658. See article by Casey Luskin here:

http://www.evolutionnews.org/2009/11/truth_or_dare_with_dr_ken_mill027891.html

Retrieved 28th April 2013.

[18] Joseph Levine & Kenneth Miller, Biology: Discovering Life (1st ed., D.C. Heath and Co., 1992), pg. 152; (2nd ed. D.C. Heath and Co., 1994), p. 161.

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OPERA or Soap Opera?

April 22, 2013

In the post Dr. Ben Goldacre and the Reproducibility of Scientific Research, I discussed a systemic problem within contemporary science, viz. publication bias. Not all results of scientific research are published; results that stray uncomfortably far from sundry paradigms are sometimes not even submitted by their authors to journals.

A reader objected to this, citing the OPERA experiment as an example of negative results being fearlessly published. Matt wrote:

But I can provide you with countless examples of the researchers deciding to put their results out to the larger community anyway… even at the risk of humiliation if they are found to have messed up. For a recent example, look up the “superluminal neutrino” results from the OPERA experiment.

I didn’t need to look up the OPERA episode, being very familiar with it. But that sorry affair has little in common with the theme of the post Dr. Ben Goldacre and the Reproducibility of Scientific Research, as will be seen in this post.

***

OPERA stands for Oscillation Project with Emulsion tRacking Apparatus. In September 2011, the experiment electrified the world with the announcement that superluminal neutrinos – subatomic particles that travel faster than light – had been discovered. Physicists usually respond to such grand claims with a laconic “Important, if true.” In this case, had the results been correct, they would not just be important; they would “kill modern physics as we know it”, as Laura Patrizii, leader of OPERA’s Bologna group, put it. The story ended ignominiously, if predictably. The results were found to be incorrect, partly due to some loose cables. But let’s begin at the beginning.

Modern physics is often done by large groups of scientists working together. When you have large collaborations like the OPERA group, it’s prudent to seek consensus before making announcements about the research. Dmitri Denisov, a physicist at Fermilab in Batavia, Illinois, says it is standard procedure to wait to publish a paper until everyone in the collaboration has signed on. “We really strive to have full agreement,” he says. “In some cases it takes months, sometimes up to a year, to verify that everyone in the collaboration is happy.” In the case of OPERA, 15 of the 160 members refused to add their names to the original paper because they felt the announcement and submission of the results for publication were premature. “I didn’t sign because I thought the estimated error was not correct,” said team member Luca Stanco of the National Institute of Nuclear Physics in Italy. In a New Scientist article, Stanco was quoted as saying that “We should have been more cautious, more careful, presented the result in not such a strong way, more preliminarily. Experimentalists in physics can make mistakes. But the way in which we handle them, the way we present them – we have some responsibility for that.” Physics World mentioned Caren Hagner, leader of the OPERA group at Hamburg University and one of the people whose name did not appear on the pre-print. She too argued that the collaboration should have carried out the extra checks before submitting the paper for peer review.

The OPERA operatives were in such a rush to announce their scoop to the world that they failed to apply basic prudence. Janet Conrad, a particle physicist at MIT, said that much of the negative reaction from the physics establishment to the announcement stemmed from the fact that there were insufficient experimental checks carried out prior to the announcement. “A [paper in] Physical Review Letters is four pages long. An experiment is vastly more complicated than that,” she says. “So we have to rely on our colleagues having done all of their cross checks. We don’t expect to make a retraction within a year.” Fermilab’s Joseph Lykken concurred. “Precisely because these are big, complicated experiments, the collaborations have a responsibility to both the scientific community and to the taxpayers to perform due diligence checks of the validity of their results,” he said. “The more surprising the result, the more time one must spend on validation. Anyone can make a mistake, but scientific collaborations are supposed to catch the vast majority of mistakes through internal vetting long before a new result sees the light of day.” CERN physicist Alvaro De Rujula also had strong words in this regard. “The theory of relativity is exquisitely well-tested and consistent. Superluminal neutrinos were far, far too much in violation of the rules to be believed, even for a nanosecond. That ought to have made the OPERA management have everything checked even more carefully. Alas, it turned out not to be a subtle error, but mainly a bad connection, the very first thing one checks when anything misbehaves.”

Then, again in violation of good practice, the OPERA results were announced to the press rather than first presented to peers through the usual science channels. The physicist Lawrence M. Krauss, director of the Origins Project at Arizona State University (and an ardent atheist) authored an op-ed in the Los Angeles Times entitled Colliding Theories, with the subtitle Findings that showed faster-than-light travel were released too soon. He wrote,

What is inappropriate, however, is the publicity fanfare coming before the paper has even been examined by referees. Too often today, science is done by news release rather than waiting for refereed publication.

What makes all of this even more surprising is that the OPERA collaboration did not have a direct competitor from which a scoop had to be snatched. The physicists were in a position to carefully check and re-check their results before rushing off to make their announcement.

As a result of the fiasco, OPERA spokesman Antonio Ereditato of the University of Bern in Switzerland and experimental coordinator Dario Autiero of the Institute of Nuclear Physics in Lyon, France, resigned following a 16-13 no-confidence vote from the collaboration’s other leaders. An indication of just how embarrassing this episode was for physics is that CERN (European Centre for Nuclear Research), the European collaboration that supplied the neutrinos to the OPERA experiment, had no official comment on the resignations, distancing itself from the OPERA experiment despite its central role in publicizing the original results. Physics World reported that a press officer for CERN refused to be identified and emphasised that OPERA was “not a CERN collaboration” since it “only sends [OPERA] a beam of neutrinos.”

To some extent, the OPERA debacle was about grabbing headlines. As one report put it,

If faster than light neutrinos do exist, there need to be many rounds of testing, independent analyses and rigorous peer review before we can start announcing dents in Einstein’s bedrock theories. But, as is abundantly clear in this world of fierce media competition, social media and science transparency, any theory is a good theory so long as it makes a good story — as long as the scientific method has been followed and the science is correctly represented by the writer, that is. [Italics in the original.]

***

Let us digress for a moment to discuss a few points that are relevant to material discussed in Genesis and Genes, before returning to the topic of publication bias.

I explained in Genesis and Genes that the public almost always misunderstands what is meant by “measurement” in the context of contemporary science. Measurements in cosmology and physics do not mean that someone is doing something as prosaic and straightforward as reading a temperature off a thermometer. The procedure is far more complicated, and introduces enormous amounts of complexity into the endeavour. This is something that Professor Krauss stressed in the article he penned for the LA Times:

The claim that neutrinos arrived at the Gran Sasso National Laboratory in Italy from CERN’s Large Hadron Collider in Switzerland on average 60 billionths of a second before they would have if they were traveling at light speed relies on complicated statistical analysis. It must take into account the modeling of the detectors and how long their response time is, careful synchronization of clocks and a determination of the distance between the CERN accelerator and the Gran Sasso detector accurate to a distance of a few meters. Each of these factors has intrinsic uncertainties that, if misestimated, could lead to an erroneous conclusion.

Informed consumers of science realise that words like measure – which convey a high degree of certainty to the public – in reality reflect something far murkier. This is why, in the post Missing Mass, I pointed out that cosmology is much more theory than observation. The public, inasmuch as it knows anything about the expansion of the universe, for example, entertains fantasies about astronomers watching galaxies flying off into the cosmic sunset, like an airplane slowly moving across the distant horizon. That’s nonsense. To “measure” the expansion of the universe, inferences are made on the basis of complex statistical analyses which depend on layer upon layer of assumption and analysis. In Genesis and Genes, I discussed the work of the brilliant mathematician and member of the National Academy of Sciences Irving Segal. I wrote that,

The most recent study by Segal and his colleagues contained a detailed analysis of Hubble’s law based on data from the de Vaucoleurs survey of bright cluster galaxies, which includes more than 10 000 galaxies. (It is worthwhile noting that Edwin Hubble’s own analysis was based on a puny sample of twenty galaxies.) The results are astounding. The linear relationship that Hubble saw between redshift and apparent brightness could not be seen by Segal and his collaborators. “By normal standards of scientific due process,” Segal wrote, “the results of [Big Bang] cosmology are illusory.”

The debate between Segal and his detractors was not about who had more acute eyesight; it was about ultra-complex models and statistical analysis. This should give informed consumers of science pause when they encounter reports of “measurements” in cutting-edge science.

***

I pointed out in Genesis and Genes that there exists a misconception of science as the ultimate cosmopolitan pursuit, devoid of any nationalistic flavour which might influence research. The truth is that, being a human endeavour, such factors do influence scientific research. Remember the part about acupuncture? I wrote,

Between 1966 and 1995, there were forty-seven studies of acupuncture in China, Taiwan, and Japan, and every trial concluded that acupuncture was an effective medical treatment for certain conditions. During the same period, there were ninety-four clinical trials of acupuncture in the United States, Sweden, and the United Kingdom, and only fifty-six per cent of these studies found any therapeutic benefits.

Controlled, double-blind clinical trials are not magic bullets. One’s cultural background influences research, and this was a factor in OPERA also. One news item states that “The large international collaboration has had to contend not just with the usual personality conflicts, but also with cultural differences between Italian, Northern European, and Japanese scientists. The added scrutiny from the controversial result exacerbated those tensions.”

***

At any rate, the OPERA experience has little to do with ordinary, day-to-day publication bias. Once OPERA produced a tsunami of publicity with its premature announcement of superluminal neutrinos, its leaders had no choice but to come clean about the various failures that plagued their experiment. Back on the ranch, far from the limelight, the fact is that uncomfortable results are often just ignored, exiled to distant directories in one’s hard-drive. They don’t make headlines; they don’t provoke resignations; they just don’t get reported and published. And that produces a distorted picture in the minds of scientists and the public with regards to important issues. In the article by Professor Krauss in the LA Times, Kraus – who is an enthusiastic adherent of scientism – writes that

What is inappropriate, however, is the publicity fanfare coming before the paper has even been examined by referees. Too often today, science is done by news release rather than waiting for refereed publication. Because a significant fraction of experimental results ultimately never get published or are not later confirmed, providing unfiltered results to a largely untutored public is irresponsible. [Emphasis added.]

One can quibble with Krauss regarding how much filtering – this is a synonym for prejudice – must be done to protect the public from unorthodox research findings. But the fact is that a significant portion of research is never published. One reason for this is that researchers are trapped in paradigms that stain certain research results as wrong. As Nottingham University astronomer Michael Merrifield explains,

And, more worrying, is something that scientists like to push under the carpet… there’s psychology in this as well. If, in 1985, I made a measurement of the distance [from the Sun] to the centre of the galaxy when everyone said it was ten kilo-parsecs, and I got an answer that said it was seven kilo-parsecs, I would have thought, “Well, I must have done something wrong” and I would have stuck it in some filing cabinet and forgot about it; whereas if I had got an answer that agreed with the consensus, I’d probably have published it… In this error process, there’s also psychology. As I say, scientists are very uncomfortable about this, because we have this idea that what we are doing is objective and above such things. But actually, there is a lot of human interaction and psychology in the way we do science.

Some in the science establishment try to avoid confronting this reality by invoking ideal worlds, in which various safeguards eliminate any residual doubt from experiments. But scientific research – like virtually all human activity – is more ambiguous than these scientists would have you believe. In Genesis and Genes I quoted the physicist and philosopher Sir John Polkinghorne:

Many people have in their minds a picture of how science proceeds which is altogether too simple. This misleading caricature portrays scientific discovery as resulting from the confrontation of clear and inescapable theoretical predictions by the results of unambiguous and decisive experiments… In actual fact… the reality is more complex and more interesting than that.

***

Nobody doubts that there are many sincere politicians out there. And nobody denies that there is a gaping gulf between election-season promises and post-election reality. After the debris of elections is cleared and the votes tallied, the real, gritty, grey world of horse-trading, budgetary constraints, political alliances and a host of other factors intervene to make politicians, well, politicians.

Science – including the realm of the hard sciences – is a human endeavour. Scientific research is subject to a galaxy of factors beyond the nuts and bolts of the laboratory. It is affected by every condition related to human nature. OPERA is a good example of an experiment going awry because of mundane weaknesses such as impulsivity, the pursuit of glory and bad judgment. But the fact that scientific research happens in the real world and not in some idealized version thereof is just as true in the day-to-day research that never makes headlines.

Informed consumers of science recognise this, and recognise the limitations that these weaknesses impose upon the credibility of scientific research. Science is strong – though never infallible – when it explores phenomena that are repeatable, observable and limited. Its credibility diminishes rapidly as it meanders from these parameters. And when science makes absolute statements about the history of the universe or life, you should take them with a sack of salt.

***

See also:

The post Dr. Ben Goldacre and the Reproducibility of Research:

https://torahexplorer.com/2013/04/10/dr-ben-goldacre-and-the-reproducibility-of-research/

The post Missing Mass:

https://torahexplorer.com/2013/03/07/missing-mass/

References:

The quotations about OPERA in this post come from the following sources:

http://news.discovery.com/space/opera-leaders-resign-after-no-confidence-vote-120404.htm

http://news.discovery.com/space/faster-than-light-neutrino-theory-almost-certainly-wrong-111012.htm

http://www.newscientist.com/article/dn21093-fasterthanlight-neutrino-result-to-get-extra-checks.html

http://www.newscientist.com/article/dn21656-leaders-of-controversial-neutrino-experiment-step-down.html

http://articles.latimes.com/2011/oct/04/opinion/la-oe-krauss-neutrino-20111004.

http://physicsworld.com/cws/article/news/2011/oct/07/tension-emerges-within-opera-collaboration

Retrieved 21st April 2013.

Professor Merrifield can be watched here:

 http://www.youtube.com/watch?v=gzvPH6A5CmQ

The Limits of Variability

April 16, 2013

Evolutionary theory is based on a number of crucial assumptions. One of the most important of these assumptions is that biological organisms are infinitely plastic – they can accumulate an endless number of mutations and be gradually transformed into different organisms. After all, if an ancient one-celled organism eventually begot creatures that possess brains, gills, wings, immune systems, antlers, capillaries and countless other features, the process must have involved millions of mutations that stretched organisms beyond recognition.

Nobody denies that there is some flexibility within life forms. Breeders exploit this biological malleability to enhance desirable features – more colourful crests in pigeons or tennis-ball-sized peaches. But this is a far cry from the flexibility that is required to allow an organism to accumulate mutations to the point where new organs and body plans emerge. That level of plasticity is indispensable to evolutionary theory. The co-discoverer of Natural Selection, Alfred Russel Wallace, called his 1858 essay “On the Tendency of Varieties to Depart Indefinitely from the Original Type”. The operative word here is indefinitely.

But infinite plasticity is an assumption – there is no evidence that biological organisms can change beyond very narrow limits. One of the architects of Neo-Darwinism, Theodosius Dobzhansky, emphasised the differences between micro-evolution (the small, intra-species events that are observed in nature and in breeding programs) and macro-evolution (the emergence of new organs and body plans). As I wrote in Genesis and Genes,

In 1937, Dobzhansky noted that there was no hard evidence to connect small-scale changes within existing species (which he called microevolution) to the origin of new species and fundamentally-new structures (an eye or a wing where there hadn’t been one before) and body plans that are recorded in the fossil record (which he called macroevolution).

Dobzhansky clearly acknowledged that it is nothing but an assumption and a working hypothesis that the accumulation of micro-evolutionary changes can account for macro-evolution.

For centuries, breeders have tried to push the limits of biological variability, with little success. Norman Macbeth, in his book Darwin Retried, quotes Luther Burbank (1849-1926), who was called “the most competent breeder of all time”. Burbank worked in Santa Rosa, California in the early decades of the 20th century, and his work was funded by Andrew Carnegie. Burbank wrote that,

I am willing to admit that it is hopeless to try to get a plum the size of a small pea or one as big as a grapefruit. I have daisies on my farms little larger than my fingernail and some that measure six inches across, but I have none as big as a sunflower and never expect to have. I have roses that bloom pretty steadily for six months in the year, but I have none that will bloom twelve, and I will not have. In short, there are limits to the development possible…[1]

The biologist Julian Huxley (grandson of Darwin’s Bulldog, Thomas Huxley) made much the same point as Burbank:

In spite of intensive and long-continued efforts, breeders have failed to give the world blue roses and black tulips. A bluish purple and a deep bronze in the tulip are the limits reached. True blue and jet black have proved impossible.[2]

Huxley attributed this limit to a “lack of modificational plasticity” – variation can only go so far.

Thomas Hunt Morgan (1866-1945) was one of the founders of genetics, and received a Nobel Prize for his work.[3] Working in the famous Fly Room that he established at Columbia University, Morgan used artificial selection to try to increase the number of bristles in fruit flies. He found that the bristle number reached a maximum and could not be increased further, no matter how much selection pressure was applied.

In The Natural Limits of Biological Change, Lane P. Lester and Raymond G. Bohlin quoted the noted French biologist Pierre Grassé (1895-1985):

What is the use of their [E. Coli] unceasing mutations if they do not change? In sum, the mutations of bacteria and viruses are merely hereditary fluctuations around a mean position; a swing to the right, a swing to the left, but no final evolutionary effect.[4]

In Genesis and Genes, I mentioned Lynn Margulis (1938-2011) a number of times. A world-famous biologist, she was elected to the United States National Academy of Sciences in 1983 and inducted into the World Academy of Art and Science, the Russian Academy of Natural Sciences, and the American Academy of Arts and Sciences between 1995 and 1998. She was the recipient of the William Procter Prize for Scientific Achievement (1999) and was awarded the National Medal of Science by President Bill Clinton in that same year. Margulis was an evolutionist, but she rejected Neo-Darwinism partly because of her perception that the standard picture of new species being formed as a result of the accumulation of mutations was false. In an interview in Discover Magazine, she said:

… neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change – led to new species. I believed it until I looked for evidence.

Margulis makes the point that Neo-Darwinism requires that biological organisms be infinitely-plastic – just pile mutation upon mutation and you’ll eventually get a new species. She explains why this is unrealistic:

This is the issue I have with neo-Darwinists: they teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.[5]

Dr. Lee Spetner[6] echoes this observation:

Degrading side effects have also been noted in insects that have become resistant to insecticides. M. W. Rowland from the Rothamsted Experimental Station in Hertforshire, England has reported that mosquitoes that have become resistant to dieldrin are less active and slower to respond to stimuli than are other insects.[7] Their resistance to the insecticide is thus bought at the price of a more sluggish nervous system…

In grain, selection for high protein content has been found to result in less starch per seed and less grain per planting.[8] Dairy cattle bred for high milk production turn out to be less fertile than normal cattle.[9]

This effect – that every “advantageous” genetic trait is bought at the expense of some other trait, a case of stuffing your right pocket with notes taken from your left pocket – is recognised by world-famous scientists whose fealty to the evolutionary paradigm is uncontested. Thus, E.O. Wilson writes that,

Artificial selection has always been a tradeoff between the genetic creation of traits desired by human beings and an unintended but inevitable genetic weakness in the face of natural enemies.[10]

And Ernst Mayr wrote that,

The most frequent correlated response of one-sided selection is a drop in general fitness. This plagues virtually every breeding experiment.[11]

As I wrote in Genesis and Genes:

Whether it is the finches’ beaks, or minuscule growth in the length of frogs’ feet, or slight colouration variations between moths, or minor changes to the genomes of bacteria, or elephant tusk size as measured by the Uganda Game Department between 1925 and 1958, or the change in head size of a Mediterranean lizard, Podarcis sicula, between 1971 and 2008 as registered by a Belgian team studying the lizard population on a pair of little islands off the Croatian coast[12], the claims far outstrip the evidence.

Finally, here is what the delightful David Berlinksi had to say on the subject, as quoted in Genesis and Genes,

Changes in wing color and the development of drug resistance are intraspecies events. The speckled moth, after all, does not develop antlers or acquire webbed feet, and bacteria remain bacteria, even when drug-resistant… the grand evolutionary progressions, such as the transformation of a fish into a man, are examples of macro-evolution. They remain out of reach, accessible only at the end of an inferential trail.

***

Informed consumers of science are aware that the grand evolutionary story is crucially dependent on the alleged ability of biological organisms to change without limit. The oft-repeated claim about overwhelming evidence heard in the context of evolution is indeed true, but not in the way it is usually intended. There is overwhelming evidence – from the field, the farm and the laboratory – for the fact that living creatures cannot change beyond narrow limits.

***

See Also:

The post Birds and Micro-Evolution:

https://torahexplorer.com/2013/04/07/birds-and-micro-evolution/

 The post An Interview with Lynn Margulis:

https://torahexplorer.com/2013/02/25/an-interview-with-lynn-margulis/

 The post More on Margulis:

https://torahexplorer.com/2013/02/26/more-on-margulis/

References:

[1] Norman Macbeth, Darwin Retried, Dell Publishing, 1973, page 36. I came across the quotations from this book in an essay by Tom Bethell on the website Evolution News and Views. See http://www.evolutionnews.org/2012/04/natural_limits058791.html.

Retrieved 15th April 2013.

[2] Julian Huxley, Evolution: The Modern Synthesis, London, Allen and Unwin, 1943, page 519.

[3] “American zoologist and geneticist, famous for his experimental research with the fruit fly (Drosophila) by which he established the chromosome theory of heredity. He showed that genes are linked in a series on chromosomes and are responsible for identifiable, hereditary traits. Morgan’s work played a key role in establishing the field of genetics. He received the Nobel Prize for Physiology or Medicine in 1933.”

Morgan, Thomas Hunt. (2009). Encyclopædia Britannica. Encyclopædia Britannica 2009 Ultimate Reference Suite.  Chicago: Encyclopædia Britannica.

[4] Pierre Grassé, Evolution of Living Organisms, 1977, quoted in Lane P. Lester and Raymond G. Bohlin, The Natural Limits of Biological Change, Zondervan Publishing, 1984, page 149.

[5] The interview can be read online:

http://discover.coverleaf.com/discovermagazine/201104?pg=68#pg70

Retrieved 25th February 2013.

[6] Lee Spetner, Not By Chance!, The Judaica Press, 1997, pages 144-148.

[7] Rowland, M.W. (1987). Fitness of Insecticide Resistance, Nature, volume 327, page 194.

[8] Brock, R.D. (1980). Mutagenesis and Crop Production, in Carlson, P.S., The Biology of Crop Productivity, New York: Academic Press, pages 383-409.

[9] Hermas, S.A. (1987). Genetic relationships and additive genetic variation of productive and reproductive traits in Guernsey dairy cattle, Journal of Dairy Science, volume 70, pages 1252-1257.

[10] Wilson, E.O. (1992). The Diversity of Life, Cambridge, Harvard University Press.

[11] Ernst Mayr, Populations, Species, and Evolution, Harvard University Press, 1970, page 163.

[12] The last two examples come from Richard Dawkins’ book The Greatest Show on Earth: The Evidence for Evolution. The chapter containing the discussion of the elephant tusks and the lizards’ heads is bombastically entitled [Evolution] Before Our Very Eyes.

Dr. Ben Goldacre and the Reproducibility of Research

April 10, 2013

The institution of peer-reviewed, published research is not a magic wand that ensures that all findings are disseminated to all relevant parties. I wrote in Genesis and Genes about an important paper that appeared in Nature in March 2012:

During a decade as head of global cancer research at Amgen, [Glenn] Begley identified 53 “landmark” publications – papers in top journals, from reputable labs – for his team to reproduce. Begley sought to double-check the findings before trying to build on them for drug development. Result: 47 of the 53 studies (89%) could not be replicated. He described his findings in a commentary piece published in the journal Nature in March 2012. In a Reuters report, Begley said “It was shocking. These are the studies the pharmaceutical industry relies on to identify new targets for drug development… As we tried to reproduce these papers we became convinced you can’t take anything at face value.” Begley’s experience echoes a report from scientists at Bayer AG. In a 2011 paper titled Believe it or not, they analyzed in-house projects that built on “exciting published data” from basic science studies. “Often, key data could not be reproduced,” wrote Khusru Asadullah, vice president and head of target discovery at Bayer HealthCare in Berlin, and colleagues. Of 47 cancer projects at Bayer during 2011, less than one-quarter could reproduce previously reported findings, despite the efforts of three or four scientists working full time for up to a year. Bayer dropped the projects.

Bayer and Amgen found that the prestige of a journal was no guarantee a paper would be solid. “The scientific community assumes that the claims in a preclinical study can be taken at face value,” Begley and Lee Ellis of MD Anderson Cancer Center wrote in Nature. They and others fear the phenomenon is the product of a skewed system of incentives that has academics cutting corners to further their careers. Part way through his project to reproduce promising studies, Begley met for breakfast at a cancer conference with the lead scientist of one of the problematic studies. “We went through the paper line by line, figure by figure,” said Begley. “I explained that we re-did their experiment 50 times and never got their result. He said they’d done it six times and got this result once, but put it in the paper because it made the best story. It’s very disillusioning.”

A reader has now kindly drawn my attention to a TED talk by Dr. Ben Goldacre.[1] The talk is entitled What Doctors Don’t Know about the Drugs they Prescribe. [Goldacre refers to the Nature paper mentioned above at about 02:00]. The points made by Dr. Goldacre are relevant to all branches of science.

Early on in the talk, Dr. Goldacre refers to a case study of the drug Lorcainide. This drug was designed to suppress arrhythmia, irregular beating of the heart. It was thought that since patients often suffer from arrhythmia after a heart attack, suppressing irregular heart-beating may be salubrious. In a preliminary study, fifty heart-attack patients were given Lorcainide, while another fifty patients were given a placebo. In the first group, ten patients died; in the second, only one patient died. The researchers concluded that Lorcaininde was dangerous. But because this trial was deemed a failure – the drug had no commercial prospects – the study was never published. This had tragic consequences. Not knowing the results of the unpublished study, other research groups in the following years who also thought that arrhythmia-suppressing drugs have medical potential brought similar medicines to market. According to Goldacre, this led to the unnecessary death of more than 100 000 patients.

A little further in his talk Dr. Goldacre discusses the drug Reboxetin, manufactured by Pfizer. With some asperity, Dr. Goldacre announces that he was misled by the published results regarding this drug, as indeed he was. Seven clinical trials were conducted to test the effectiveness of Reboxetin. One trial produced a positive result i.e. the drug produced better results than a placebo, and was published. Six trials produced negative results – and were not published. Goldacre says that he – and presumably thousands of other doctors – freely prescribed this drug on the basis of the published results.

Next, Dr. Goldacre turns to all the antidepressant trials submitted to the FDA for approval over a 15-year period. There were 38 positive trials and 36 negative trials submitted to the FDA. But when one looks at the publication record of these studies in the peer-reviewed academic literature, one finds that of the 38 positive trials, 37 were published; of the 36 negative trials, only 3 were published.

Dr. Goldacre peppers his talk with pungent comments about the rotten state of things. He says that publication bias is so prevalent that it cuts to the core of evidence-based medicine; the state of affairs “is a systematic flaw in the core of medicine”; he uses phrases like “This is a disaster” and terms like “cancer” to describe the situation.

***

The issues discussed by Dr. Goldacre in his TED talks and in his books are by no means limited to medical science. Publication bias is a systemic problem within science. One manifestation of this is that research that does not conform to basic tenets of sundry paradigms is simply not published, thus distorting the impression that scientists and the public form about important topics.

I discussed this in some length in Genesis and Genes. I pointed out that the problems begin right at the outset of one’s university training. Laboratory exercises, in which students ostensibly investigate some phenomenon, are actually exercises in reproducing textbook results.[2] I quoted the distinguished evolutionary biologist Massimo Pigliucci (who has doctorates in genetics, botany, and the philosophy of science):

Things are often only marginally better in college or university classes… Worse yet, most of these exercises are “prepackaged” labs designed to obtain a predetermined outcome, which often enough does not occur because of the carelessness of both students and teaching assistants. The latter are then tempted to do the worst thing they could possibly do in teaching science: tell the students that they should have gotten result X instead, and to write up their reports as if they had. Is it a surprise, then, that the whole enterprise becomes meaningless and that most students think science is either too difficult for them to grasp or, worse, is actually done by cooking the results to come out according to a priori expectations…

I pointed out that in the vast majority of science programs, no modules are offered in the psychology of research or the history/philosophy of science. The result is that science undergraduates who are unaware of the myriad biases which affect research become scientists who are often unaware of the biases affecting the publication of research results.

In this context, I referred to a talk given by Professor Michael Merrifield, an astronomer at Nottingham University.[3] Merrifield was discussing a purely technical issue – measuring the distance between our Sun and the centre of the Milky Way galaxy. This is not anthropology or sociology, but the research is nonetheless subject to psychological forces:

And, more worrying, is something that scientists like to push under the carpet… there’s psychology in this as well. If, in 1985, I made a measurement of the distance [from the Sun] to the centre of the galaxy when everyone said it was ten kilo-parsecs, and I got an answer that said it was seven kilo-parsecs, I would have thought, “Well, I must have done something wrong” and I would have stuck it in some filing cabinet and forgot about it; whereas if I had got an answer that agreed with the consensus, I’d probably have published it… In this error process, there’s also psychology. As I say, scientists are very uncomfortable about this, because we have this idea that what we are doing is objective and above such things. But actually, there is a lot of human interaction and psychology in the way we do science.

This phenomenon – sticking your results into a filing cabinet because they stray uncomfortably far from the consensus – is common in contemporary science. The failure to publish anomalous or “wrong” results is as prevalent in astronomy, physics or biology as it is in medical science.

Publication bias is bad science (One of the books authored by Dr. Goldacre is entitled Bad Science, and one of his TED talks is called Battling Bad Science). And awareness of this aspect of modern science is crucial in the process of becoming an informed consumer of science. The picture conveyed to the public – whether the topic is climate change, evolutionary biology, cosmology or a host of other areas – is by no means one that reflects all the research being done. It is distorted by numerous factors. Sometimes, there are financial factors (as in the case of Lorcainide); sometimes, there are political factors (an example is climate science); sometimes, there are paradigm considerations (read about Daniel Shechtman, Robin Warren and Alfred Wegener). The bottom line is that the final picture is often significantly incomplete.

***

See also:

The post Replication of Experimental Data:

https://torahexplorer.com/2013/02/10/replication-of-experimental-data/.

References:

[1] See http://www.youtube.com/watch?v=RKmxL8VYy0M.

Retrieved 10th April 2013.

[2] A reader of Genesis and Genes who trained as an aeronautical engineer wrote to me to express how, upon reading this passage in the book, he was struck by the fact that this had happened to him repeatedly throughout his university career, without his being consciously aware of the phenomenon.

[3] See http://www.youtube.com/watch?v=gzvPH6A5CmQ

Retrieved 10th April 2013.

Birds and Micro-Evolution

April 7, 2013

I devoted a substantial part of Genesis and Genes to a discussion of macro-evolution and micro-evolution. The difference is crucial. Micro-evolutionary changes are intra-species events; they are common and uncontroversial. Macro-evolutionary changes are needed to drive real biological innovation – they supposedly lead to new organs and new body plans. Macro-evolutionary changes are the stuff of common descent. If all life on Earth today arose from one or a few one-celled organisms, there had to have been untold millions of macro-evolutionary changes along the way.

The earliest references to the terms micro- and macro-evolution that I could find were made by one of the architects of Neo-Darwinism, Theodosius Dobzhansky. As I wrote,

In 1937, Dobzhansky noted that there was no hard evidence to connect small-scale changes within existing species (which he called microevolution) to the origin of new species and fundamentally-new structures (an eye or a wing where there hadn’t been one before) and body plans that are recorded in the fossil record (which he called macroevolution).[1]

 According to Dobzhansky,

There is no way toward an understanding of the mechanisms of macroevolutionary changes, which require time on a geological scale, other than through a full comprehension of the microevolutionary processes observable within the span of a human lifetime. For this reason we are compelled at the present level of knowledge reluctantly to put a sign of equality between the mechanisms of macro- and microevolution, and proceeding on this assumption, to push our investigations as far ahead as this working hypothesis will permit.

Dobzhansky clearly acknowledged that it is nothing but an assumption and a working hypothesis that the accumulation of micro-evolutionary changes can account for macro-evolution. This has been controversial right from the beginning. In 1940, Berkeley geneticist Richard Goldschmidt argued that “the facts of microevolution do not suffice for an understanding of macroevolution.”[2] Goldschmidt added that “Microevolution does not lead beyond the confines of the species, and the typical products of microevolution, the geographic races, are not incipient species.”[3] At the other end of the century, evolutionary biologists Scott Gilbert, John Opitz and Rudolf Raff wrote in 1996 that:[4]

Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest.

 Gilbert et. al concluded that, “The origin of species – Darwin’s problem – remains unsolved.”

Unfortunately, most members of the public are not aware of the enormous difference between micro- and macro-evolution. This ignorance is exploited by the evolution establishment. Numerous examples of micro-evolution are provided in newspapers, documentaries, and websites, and are then conflated with macro-evolution to foster the impression that macro-evolution has been established.

I discussed a number of examples of this phenomenon in Genesis and Genes. Readers will recall the less-than-thrilling discovery, discussed in Nature’s “evolutionary gems” online resource, regarding small birds in Southern England. Nature promised readers that they would see “marked evolutionary differentiation” at “small spatial and temporal scales.” The journal informs its readers that over a span of about 35 years, the birds known as great tits from the eastern part of the Wytham woodland saw a decrease in adult body size that amounted to a net average change of about 1 gram (less than 10 percent of total body mass). Fledgling birds likewise saw a small change in body mass. Birds in the northern part of the wood did not experience such a change.[5] Needless to say, this is hardly evidence for the grandiose claims of evolutionary biology regarding the ability of natural selection acting on random mutations to produce birds in the first place.

Here are two more recent examples of this phenomenon, both from the sphere of avian life.

A rather prosaic discovery was reported last month in Current Biology[6] and was summarised in Science Now:[7]

Cliff swallows that build nests that dangle precariously from highway overpasses have a lower chance of becoming roadkill than in years past thanks to a shorter wingspan that lets them dodge oncoming traffic. That’s the conclusion of a new study based on 3 decades of data collected on one population of the birds. The results suggest that shorter wingspan has been selected for over this time period because of the evolutionary pressure put on the population by cars.

It seems clear that shorter wings give birds better manoeuvrability:

“Probably the most important effect of a shorter wing is that it allows the birds to turn more quickly,” says [ecologist] Charles Brown [of the University of Tulsa in Oklahoma, who conducted the new study with wife Mary Bomberger Brown, an ornithologist at the University of Nebraska, Lincoln.] Previous studies on the dynamics of flight have illustrated the benefits of short wings for birds that perform many pivots and rolls during flying and shown that shorter wings also may allow the birds to take off faster from the ground, he adds.

So what’s the significance of this data-acquisition exercise?

“This is a clear example of how you can observe natural selection over short time periods,” says Brown. “Over 30 years, you can see these birds being selected for their ability to avoid cars.”

But how significant are these changes in the grand scheme of things? The report tells us that,

When the researchers analyzed the average wing length of the living birds in the population, they discovered that it had become shorter over time, from 111 millimeters in 1982 to the 106 millimeter average in 2012. The data suggested to the Browns that roadkill deaths were a major force driving this selection. Birds with longer wings would be more likely to be killed by vehicles and less likely to reproduce…

So, over 30 years, the average length of the swallows’ wings became shorter by about 5 mm, or 4.5%. Must we, um, swallow the claim that this example of natural selection, together with non-teleological mutations, is convincing evidence for the origin of birds, as well as all life-forms on earth?

***

Nature recently reported on research published in Science. The study in question was led by University of Utah biologist Michael Shapiro and offers “insight into the genetics of both ‘fancy’ domestic breeds and plain street pigeons and supports their common origin from the wild rock dove (Columba livia).”[8] The report begins with some background:

Humans have shaped the domestic pigeon into hundreds of breeds of various shapes, colours and attributes — a diversity that captivated Charles Darwin, who even conducted breeding experiments on his own pigeons. Now, a number of domestic and feral pigeon genomes have been sequenced for the first time, giving scientists a resource for studying the genetics of how these traits evolved.

 Here is what the research involved:

 The Utah team… sequenced a complete ‘reference’ genome from a breed called the Danish tumbler. The researchers also sequenced the genomes of 36 different fancy breeds and of two feral birds from different regions of the US.

 And the results:

 The study fills in knowledge about the relationships between breeds, many of which are centuries old with origins in the Middle East. Darwin argued that all domestic pigeon breeds descended from the wild rock dove. Shapiro says this study puts data behind that argument, as all the breeds sequenced are more similar genetically to one another than to another, closely related, species of pigeon, C. rupestris. It also found that street pigeons are genetically similar to racing homing pigeons, which frequently escape into the wild.

 So the wild rock dove is ancestral to many varieties of pigeons today. Now, the rock dove is just the rock pigeon, also known as the common or garden pigeon – the kind that soils your patio. So the claim being made here is that pigeons are descended from pigeons.

 But the humdrum nature of the research is obscured by the electric title of the report: Pigeon DNA proves Darwin right. Yeah, right; it also proves right every common peasant in Darwin’s time who knew that you could breed cows, dogs, cats, tulips and hundreds of other organisms and obtain modest results. These results always demonstrate micro-evolution: a slightly faster dog, a new breed of cow, a slightly brighter tulip.

 Darwin called his book On the Origin of Species. Neither before its publication nor thereafter has anyone been able to discover or demonstrate genuine macro-evolutionary changes. As I put it in Genesis and Genes,

But there is no reason at all to believe, at the outset, that there must be a seamless progression from micro to macro. If you have seen people walking in New York and you know that people have walked on the Moon, that doesn’t justify the conclusion that it must be possible to walk from New York to the Moon. Small processes – walking around your home, in our analogy – cannot necessarily be extrapolated to big processes – like walking in space. This notion is expressed in Dobzhansky’s reluctant admission that, as an assumption and a working hypothesis, biologists equate microevolution and macroevolution. It is something for which there is no logical imperative.

 ***

Related Posts:

An Interview with Lynn Margulis:

https://torahexplorer.com/2013/02/25/an-interview-with-lynn-margulis/

More on Margulis:

https://torahexplorer.com/2013/02/26/more-on-margulis/

 

References:

[1] Theodosius Dobzhansky, Genetics and the Origin of Species, 1937. Reprinted by Columbia University Press, 1982, page 12.

[2] Richard Goldschmidt, The Material Basis of Evolution, Yale University Press, 1940, page 8.

[3] Ibid. page 396.

[4] Scott F. Gilbert, John M. Opitz and Rudolf A. Raff, Resynthesizing Evolutionary and Developmental Biology, Developmental Biology 173 (1996): 357-372.

[5] See Dany Garant, Loeske E.B. Kruuk, Teddy A. Wilkin, Robin H. McCleery & Ben C. Sheldon, “Evolution driven by differential dispersal within a wild bird population,” Nature 433:60-65 (January 6, 2005), at: http://www.nature.com/nature/journal/v433/n7021/abs/nature03051.html

[6] You can read the summary here:

http://www.cell.com/current-biology/retrieve/pii/S0960982213001942

Retrieved 7th April 2013.

[7] See http://news.sciencemag.org/sciencenow/2013/03/evolution-via-roadkill.html

Retrieved 7th April 2013.

[8] See http://www.nature.com/news/pigeon-dna-proves-darwin-right-1.12334

Retrieved 5th April 2013.

A Lopsided Universe?

April 3, 2013

In 2005, Kate Land and João Magueijo at Imperial College London discovered a mysterious pattern in the radiation left over from the Big Bang. In analysing the cosmic background radiation, widely considered to constitute the remnants of the Big Bang, they discovered that instead of hot and cold spots being randomly scattered across the sky, as expected, the spots appeared to be aligned in one particular direction through space. The two cosmologists named this the Axis of Evil. Why evil? Because it undermines one of the most fundamental assumptions of cosmologists about the early universe. Modern cosmology is built on the belief that the universe is isotropic i.e. roughly the same in whatever direction you look. If cosmic radiation has a preferred direction, the assumption of isotropy – and the best theories about cosmic history – may need to be jettisoned.

In an April 2007 article, New Scientist revisited the Axis of Evil.[1] It pointed out that evidence is growing for the fact that the axis may be real, “posing a threat to standard cosmology.” The article explains that the threat arises from the fact that “According to the standard model, the universe is isotropic, or much the same everywhere.” The magazine reported that “two independent studies seem to confirm that it [i.e. the Axis of Evil] does exist.” Damien Hutsemékers of the University of Liège in Belgium analysed the polarisation of light from 355 quasars and found that as the quasars get near the axis, the polarisation becomes more ordered than expected. Taken together, the polarisation angles from the quasars seem to corkscrew around the axis. This was supported by another study. Michael Longo of the University of Michigan in Ann Arbor analysed 1660 spiral galaxies from the Sloan Digital Sky Survey and found that the axes of rotation of most galaxies appear to line up with the Axis of Evil. According to Longo, the probability of this happening by chance is less than 0.4 per cent. “This suggests the axis is real, and not simply an error in the WMAP data,” he says.

Now a report in TIME gives an update on the situation, and even more reason for informed consumers of science to treat with scepticism some of the central claims of modern cosmology.[2] TIME reports on a brand-new image of the early universe released by the Planck satellite mission which “poses a mystery that could shake the foundations of cosmology.” For the uninitiated, TIME explains that “For decades, scientists have operated on the assumption that the universe should look the same, on average, in all directions—same number of galaxies, sprinkled about the sky in the same general pattern, no matter where you look. It’s a homogeneity which is in keeping with a birth blast that radiated out uniformly and at once [i.e. the Big Bang].” But this newest snapshot of the universe confounds this expectation. TIME:

The ancient, leftover light from the Big Bang, however, seems lopsided, with a huge swath of sky at a slightly cooler temperature than the rest. It could simply be a fluke, like getting 50 heads in a row in a coin toss. Or it could mean that the age-old assumption about cosmic uniformity is wrong. The chance is maybe one in a few hundred that this asymmetry could happen randomly, says [Rachel] Bean [a Cornell astrophysicist].

TIME then refers to the research I cited in Genesis and Genes in connection with the Axis of Evil. It points out that “this [the Planck satellite data] isn’t an entirely new finding: it was reported a decade ago by NASA’s Wilkinson Microwave Anisotropy Probe (WMAP) satellite. There was always a chance, though, that it was some sort of mistake—but not anymore.”

At this point, the speculation begins regarding the anomalous data. For example, some scientists suggest that the universe is rotating. But the report acknowledges that these conjectures are “inconsistent with other data.” Of course, the future may bring new explanations of the WMAP and Planck data that will be consistent with standard Big Bang cosmology. Then again, there is also the distinct possibility that one of the most important pillars on which contemporary cosmology stands is, in fact, illusory.

As I pointed out in the post Missing Mass[3], most members of the public simply have no idea of the number of assumptions made in modern cosmology, and the extent to which the definitive statements of cosmologists about the age and nature of the universe are dependent on these assumptions. So often in the past, as I showed in Genesis and Genes, assumptions of this kind were accepted uncritically by one generation of scientists, only to be shown by a later generation to have been wholly unrealistic. The result was a paradigm shift. One should be parsimonious in one’s use of terms like proof or demonstration in the context of cosmology.

References:

[1] New Scientist, 14th April 2007, Vol. 194 Issue 2599, page 10.

[2] http://science.time.com/2013/03/28/look-close-somethings-strange-in-the-photo-of-the-universe/.

Retrieved 3rd April 2013.

[3] https://torahexplorer.com/2013/03/07/missing-mass/