Truth in Science

Truth in Science
The Changing Face of Pseudogenes Print E-mail
Pseudogenes are DNA sequences that resemble protein-coding genes but they are not transcribed to a messenger RNA (mRNA) in a way that could then be translated into some functional protein. Many have suggested that pseudogenes are simply molecular fossils that illustrate and provide evidence for evolutionary history. Times are changing. The non-protein coding genome was once described by the now redundant term “Junk DNA” and it is becoming increasingly apparent that non-protein coding DNA including the pseudogenes may perform important biological roles. A new article on pseudogenes can now be found on this website.
A Lesson in Cynicism Print E-mail

The current issue of New Scientist [12th July 2008] carries an editorial entitled “A lesson in cynicism”. This relates to the law recently passed by the state of Louisiana. The editorial suggests:

Now, according to supporters of the Louisiana Science Education Act, which became a state law two weeks ago, academic freedom is what elementary and secondary school teachers and school board officials need in order to pursue an "open discussion of scientific theories" with their students. Not surprisingly, given the law's originators on the religious right ("Evolution, global warming and cloning: up for grabs in Louisiana"), it places evolution at the top of the list of theories now open for discussion. It then makes provision for teachers to introduce books and other materials from outside the standard curriculum to help students "critique" the science they are taught.

In addition, the magazine includes a special report entitled “Class Conflict”  written by Amanda Gefter which describes the campaign led by Barbara Forrest [Professor of Philosophy at Southeastern Louisiana University] that attempted to prevent the bill from becoming law. For the sake of clarity and completeness, we include the actual text from the Louisiana legislation:


To enact R.S. 17:285.1, relative to curriculum and instruction; to provide relative to the teaching of scientific subjects in public elementary and secondary schools; to promote students' critical thinking skills and open discussion of scientific theories; to provide relative to support and guidance for teachers; to provide relative to textbooks and instructional materials; to provide for rules and regulations; to provide for effectiveness; and to provide for related matters.

Be it enacted by the Legislature of Louisiana:

Section 1 R.S. 17:285.1 is hereby enacted to read as follows:

285.1 Science education; development of critical thinking skills

A. This Section shall be known and may be cited as the "Louisiana Science Education Act."

B. (1) The State Board of Elementary and Secondary Education, upon request of a city, parish, or other local public school board, shall allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including evolution, but not limited to evolution, the origins of life, global warming, and human cloning.

(2) Such assistance shall include support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied, including those enumerated in Paragraph (1) of this Subsection.

C. A teacher shall teach the material presented in the standard textbook supplied by the school system and thereafter may use supplemental textbooks and other instructional materials to help students understand, analyse, critique and review scientific theories in an objective manner, as permitted by the city, parish, or other local public school board.

D. This Section shall not be construed to promote any religious doctrine,promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or nonreligion.

E. The State Board of Elementary and Secondary Education and each city, parish, or other local public school board shall adopt and promulgate the rules and regulations necessary to implement the provisions of this Section prior to the beginning of the 2008/2009 school year.

Accordingly, the law allows for the promotion of “critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including evolution, but not limited to evolution, the origins of life, global warming, and human cloning.”  Moreover, teachers are required to teach first from the standard textbooks and not to promote any religious doctrine. However, the New Scientist editorial continues:
Even for the broad concept of academic freedom this is a mighty stretch, and a corrosively cynical one. It takes a cherished feature of science - the unrestricted nature of rational inquiry - and turns it on its head to promote a non-rational agenda.
It is interesting to consider some of the definitions of cynicism that are available on the web. One definition is as follows: “An attitude of scornful or jaded negativity, especially a general distrust of the integrity or professed motives of others: the public cynicism aroused by governmental scandals”. We wonder if the New Scientist would want to include the state of Louisiana here as an example of a governmental scandal. The editorial concludes:
This time engagement is essential. The fact that academic freedom bills were introduced in six US states this year, and that the one in Louisiana received nearly unanimous support, demonstrates the gulf that exists between how scientists perceive reality and how some politicians do. That's why it is not enough for scientists to assert that evolution is correct or global warming is real: scientists and educators need to help people understand what constitutes scientific thinking.
One question - who is actually being cynical here?
Platypus: A Darwinian Cautionary Tale Print E-mail

The platypus is an evolutionary enigma and we encourage you to read the new technical article that has just been posted on the Truth in Science Website. For according to Professor Tom Kemp:

The greatest mystery of all concerning mammalian evolution stretches back for 200 years: the question of what exactly the monotreme mammals are, and how they relate phylogenetically to therians [from T.S. Kemp (2007) The Origin and Evolution of Mammals Oxford University Press pages 173-174].

Mammals comprise three major groups. The therians [theria] include all placental mammals [eutheria] and marsupials [metatheria] which have the characteristic pouch in which the immature foetus is nurtured after birth. The third group of mammals are the monotremes or egg-laying mammals. These are the prototheria [as distinct from the theria] and there are only three species of monotremes living today, only found in Australia. These are the platypus [Ornithorhyncus], the short beaked echidna [Tachyglossus] and the long-beaked echidna [Zaglossus].

Is it a reptile?

At one time, it was believed that the monotremes were transitional between reptiles and mammals. It is easy to see why. The prototheria [Gk: first beast] lay small round eggs and have some other reptilian features. For example, the male platypus possesses a spur on its hind limbs through which it delivers a venomous cocktail which contains proteins that are similar to those found in snakes. Nevertheless, the main reason that monotremes cannot be considered intermediate between reptiles and mammals is the current Darwinian consensus that reptiles and mammals have evolved independently from a putative common ancestral amniote either via the synapsid [leading to mammals] or sauropsid [leading to reptiles and birds] lineages. We refer you also to the article “Synapsids and the Evolution of Mammals” which can be found here.

Since the recent publication [May 2008] of the platypus genome in the journal Nature there has been a great deal of activity in the academic press and in the popular media including the BBC.

Is it a bird?

All this activity, however, has not brought any resolution to the evolutionary enigma that is the platypus. If anything, the situation has become even more confused. Even though there is no doubt that the platypus is a mammal, there are many genetic features that are more like birds. For example, since the platypus lays eggs, there is an ongoing requirement for active yolk production and this is reflected in its genes. Perhaps the most remarkable feature of the platypus genome, however, is the structure and number of sex chromosomes. Typically, all male mammals have one X and one Y chromosome whereas females possess two X chromosomes. The male platypus has five X and five Y chromosomes and the female platypus five pairs of X chromosomes. In most mammals, the Y chromosome possesses a gene called SRY which is a major sex determining factor but this appears to be absent in the platypus. Sex determination in the platypus is therefore something of a mystery and a great deal of research is continuing in order to discover its mechanism. Elizabeth Finkel has written a recent review of this research entitled “Genome speaks to Transitional Nature of Monotremes” in the prestigious American journal Science in which she states:

The genome sequence now shows that one of the platypus X chromosomes [X5] has more than just that one bird gene: It's almost entirely equivalent to the chicken Z chromosome.

Of course, there are also other genetic features that are unique to the platypus. These include the possession of all the biology required for the exquisitely sensitive chemical and electrical detection systems in its leathery bill. In particular, researchers have discovered numerous genes coding for odour receptors. Similar genes are found in many other mammals that rely on a sense of smell, the dog being a classic example. The platypus, however, requires this sensitivity underwater.

Thus, the platypus remains an enigma. Is it from a sauropsid lineage which includes reptiles and birds? Is it from a synapsid lineage which supposedly led to the emergence of the mammals? Or is it derived independently from some unknown ancestral amniote? Or could it be that the Darwinian hypothesis, cladistic analysis or any other classification system for that matter is just far too restrictive? The platypus is a Darwinian cautionary tale. Is it a bird or is it a plain … old platypus?

To read the full article on the platypus – go here.

Cambridge Professor writes History of Intelligent Design Print E-mail

The Laurence Professor of Ancient Philosophy at the University of Cambridge, David Sedley, has published a scholarly account of the debate over intelligent design among classical philosophers.

“David Sedley’s treatment of ancient views on intelligent design will transform our current thinking”, writes Oxford University’s Dr Thomas Johansen on the book’s cover.

The book, published by the University of California Press, is titled “Creationism and its critics in antiquity”. In the preface Professor Sedley makes clear that he has a particular definition of “creationism” in mind:

What I intend by creationism is neither [creation out of nothing or creation at some past time], but rather the thesis that the world’s structure and contents can be adequately explained only by postulating at least one intelligent designer, a creator god. This is indeed the primary issue that divides modern “creationists” from their Darwinian critics. It also divided the greatest thinkers of antiquity.

As a history from 500 to 300 BC, this book is a powerful refutation of the view that intelligent design was invented in the United States in the late 1980s.

The arguments between ancient philosophers have a surprisingly modern ring, as Dr Armand Leroi (evolutionary biologist at Imperial College London) points out in his review in Nature [Nature 452, 153 (13 March 2008)]:

Listen to Empedocles describing a time when the world was filled with a diversity of creatures with improbable combinations of features, most of which were then winnowed out, and you hear the late Stephen Jay Gould illuminating the body plans of the Burgess Shale fossils. Listen to Aristotle heaping scorn on Democritus for supposing that living things self-assemble from accidental combinations of atoms, and you hear Fred Hoyle's gambit that "a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein". Truly it has been, as Darwin said, just "one long argument".

How did the ancients argue for intelligent design? Here are two examples.

Xenophon’s Socrates would take a statue or painting, which everyone would attribute to an artist or craftsman, and argue that the human body, with its greater complexity and functionality, must have been formed by a greater artist or craftsman.

The Stoics would take Archimedes’ mechanical model of the world’s rotations in space. Even an ignorant barbarian would not doubt that this was the work of intelligence. Yet the celestial motions of the world are a vastly more complex and superior machine, and therefore we can infer that they are the work of a greater intelligence than Archimedes.

These arguments are similar to the recent argument that complex, specified information in computer programs and in the DNA of living organisms both allow us to infer intelligent design

The arguments against intelligent design in the ancient world also have close similarities to those used today. The Atomists of 3rd-1st Century BC used the idea of infinitely many worlds as a way of explaining away highly improbably structures, just as the idea of multiple universes is used today. Lucretius also used the idea of natural selection: “that accident on a sufficiently vast scale accompanied by the systematic survival of the fittest could account for the presence of apparently purposive structures in nature” (p. 151). Sedley argues that this idea was not original even to Lucretius, but that he gained it from the earlier poet Empedocles.

Clearly, the modern debate over intelligent design is not new. Professor Sedley argues that it developed when thinkers first began to question something that had previously been taken for granted: that there is a supreme governing power present in the world.

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