Tag Archives: James Shapiro

Evolution

Is There Any Scientific Controversy Over Darwinian Evolution? Part 2

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After writing part 1 of this blog post almost 3 years ago, I received several comments along the lines of, “Just because one scientist, James Shapiro, disagrees with the idea that natural selection acting on random mutations is the main engine of evolutionary change, does not mean there is a controversy.”

My goal in quoting Shapiro was not to state merely that Shapiro diverges from evolutionary orthodoxy, but to encourage the reader to go off and do some more reading to see that there are many more dissenting scientists, just like him. To help along that process, I’ve quoted from an article below that lists several more examples of the controversy. This is obviously not an exhaustive list, but is meant to lead truly curious readers to do more reading themselves. For those of you who have already decided that there is no controversy, don’t waste your time reading any further. You’ll just get more upset.

Here is Casey Luskin in an article he wrote for the Christian Research Journal titled “The New Theistic Evolutionists.” Luskin notes that

highly credible scientists doubt the neo-Darwinian view that natural selection acting on random mutation was the driving force building the complexity of life. Lynn Margulis, a member of the National Academy of Sciences, explained that “neo-Darwinists say that new species emerge when mutations occur and modify an organism,” and admitted, “I believed it until I looked for evidence.”

In 2008, sixteen leading biologists convened in Altenberg, Austria, to discuss problems with the neo-Darwinian synthesis. When covering this conference, Nature quoted leading scientists saying things like “evolutionary theory has told us little about” important events like “the origin of wings and the invasion of the land.”

That same year, Cornell evolutionary biologist William Provine explained that “every assertion of the evolutionary synthesis below is false,” including: “natural selection was the primary mechanism at every level of the evolutionary process,” “macroevolution was a simple extension of microevolution,” and “evolution produces a tree of life.”

Luskin adds:

The following year, leading biologist Eugene Koonin wrote that breakdowns in core neo-Darwinian tenets such as the “traditional concept of the tree of life” or that “natural selection is the main driving force of evolution” indicate “the modem synthesis has crumbled, apparently, beyond repair.” . . . Koonin mentioned growing skepticism over the “tree of life,” and the technical literature contains numerous examples of conflicting evolutionary trees, challenging universal common ancestry.

An article in Nature reported that “disparities between molecular and morphological trees” lead to “evolution wars” because “evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.” Another Nature paper reported that newly discovered genes “are tearing apart traditional ideas about the animal family tree,” since they “give a totally different tree from what everyone else wants.”

A 2009 article in New Scientist observes that “many biologists now argue that the tree concept is obsolete and needs to be discarded.” So severe are problems that a 2012 paper in Annual Review of Genetics proposed “life might indeed have multiple origins.”

Again, if you want to argue that there is no controversy, you are simply ignorant of what’s going on. Instead of trying to shout down any one who says there is a controversy, your time would be better spent spend studying the differing views on evolution so that you can truly understand the issues involved.

Evolution, Intelligent Design

What Questions about Evolution Have Really Been Answered?

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Post Author: Bill Pratt

Microbiologist James Shapiro, in his book Evolution: A View from the 21st Century, makes some common sense statements about the controversy over evolution. Remember that Shapiro is no young earth creationist. He is firmly entrenched as an important figure in the world of evolutionary science. Here is what Shapiro says:

General discussions of evolution, especially in the context of the “Intelligent Design” controversy, suffer from an unfortunate conflation in the minds of the lay public (and also of scientists) of three distinct questions:

• The origin of life

• The evidentiary basis for an evolutionary process

• The nature of evolutionary change

Almost universally, the term Darwinism is assumed to be synonymous with a scientific approach that has provided satisfactory answers to all three questions. It is to be hoped that, by now, you realize that these three questions are individually complex and that two of them are quite far from having coherent scientific explanations.

We have little solid science on the origin of life, in large part because there is virtually no physical record, but also because we still have gaps in our understanding of what constitute the fundamental principles of life.

As to the actual nature of evolutionary change processes, you have seen in Parts II and III [of his book] that cytogenetic observations, laboratory experiments, and, above all, molecular evidence about genome sequence changes tell us that the simplifying assumptions made in the 19th and early 20th Centuries are plainly wrong. They fail to account for the variety of cellular and genomic events we now know to have occurred. It should be emphasized that many change events have been quite rapid and have involved the whole genome—notably, symbiosis, interspecific hybridization, and whole genome doubling.

Shapiro goes on to say that he does believe that the second question has been answered.

The one issue that has effectively been settled in a convincing way is the evidence for a process of evolutionary change over the past three billion years. The reason the answer to this question is so solid is that every new technological development in biological investigation—from the earliest days of paleontology through light microscopy and cytogenetics up to our current molecular sequence methodologies—has told the same story: living organisms, past and present, are related to each other, share evolutionary inventions, and have changed dramatically over the history of the Earth.

However, little evidence fits unequivocally with the theory that evolution occurs through the gradual accumulation of “numerous, successive, slight modifications.” On the contrary, clear evidence exists for abrupt events of specific kinds at all levels of genome organization. These sudden changes range from horizontal transfers and the movement of transposable elements through chromosome rearrangements to whole genome duplications and cell fusions.

I can agree with Shapiro, on this last question, to a point. I don’t think we are clear on how all organisms are related, but we certainly understand how some organisms are related. We can also see that life forms have changed dramatically over the history of the earth. I would also agree that the second question is immensely more settled than the first and third questions.

Unfortunately, as Shapiro remarks, scientists tend to conflate all three of these questions as if they are one and the same. I am thankful that a biologist of Shapiro’s stature  has attempted to clear up this confusion.

Evolution

How Is a Mouse Different from a Man?

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Post Author: Bill Pratt 

Ever since technology advanced to the point that scientists could map out entire genomes of various animals, we have been hearing how human beings are extremely similar to other mammals at the level of genes. These similarities always make news, but I have always found these similarities to be much ado about nothing.

After all, I can see with my very own eyes that humans and mice are massively different, so when biologists told me that mice and men were basically the same, I figured that their metric for comparison was being oversold.

In a NY Times article from 2002, Nicholas Wade wrote that “only about 300 genes — 1 percent of the 30,000 possessed by the mouse — have no obvious counterpart in the human genome.” So, we are told that humans and mice are 99% similar, based on their genes.

We have also been told that virtually all the information needed to construct a plant or animal is found in the genes which code for proteins, which would imply that the instructions for constructing a mouse are 99% similar to the instructions for constructing a human. This “fact” of biology never made sense to me, as I can see that mice and humans are constructed quite differently, far more than 1% differently, however we might want to count that 1%.

James Shapiro, in his book Evolution: A View from the 21st Century, explains that I wasn’t wrong after all. There is far more to the construction of an animal than the genes that code for proteins. Shapiro states,

The traditional view has been that related species differ in their repertoire of individual “genes.” But a more contemporary Evo-Devo perspective is that much of morphological change in evolution occurs by modification of expression through alteration of enhancers and other transcriptional regulatory signals, as well as distinct patterns of epigenetic formatting.

Translation: genes are not the only determinants of evolutionary body changes. There is a whole other world behind the genes that scientists have only recently been discovering. Shapiro continues:

Comparing mice and men, the “genes” stay largely the same, but their deployment differs. The bones, ligaments, muscles, skin, and other tissues are similar, but their morphogeneses and growth follow distinct patterns. In other words, humans and mice share most of their proteins, and the most obvious differences in morphology and metabolism can be attributed to distinct regulatory patterns in late embryonic and postnatal development.

The way I read this is that if we think of a human as a “house,” and a mouse as a different “house,” it is true that both houses are constructed with wood, cinder block, nails, glass, etc. That is what the genes give us, the raw materials of the house.

And that’s interesting, as far as it goes. But the actual construction of the house involves far more than raw materials. What is more important is the architecture, the drawings, that specify how the raw materials will be used to build the house. The mouse “house” is like a 100 square feet shanty, whereas the human “house” is like a 10,000 square feet exquisite mansion.

Sure, they are made out of similar materials, but to say that the shanty and mansion are 99% similar is grossly misleading, don’t you think?

Evolution

Not Your Grandmother’s Evolution

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Post Author: Bill Pratt 

I just finished reading James Shapiro’s book, Evolution: A View from the 21st Century. Shapiro is Professor of Microbiology at the University of Chicago and a deeply influential figure in evolutionary biology.

He is not a fellow at the Discovery Institute, but, shockingly, he finds the currently popular evolutionary mechanisms of natural selection and random mutation to be woefully inadequate to explain how biological evolution occurs. Shapiro’s book is difficult reading, as he has written it, it seems to me, primarily for professional biologists. There are, however, several places in the book where he brings things back down to earth for the layperson. I’d like to share a couple of his thoughts.

Contrary to the popular view that changes in the genome occur randomly in single nucleotides, Shapiro claims that “genomic innovations occur at many different levels of complexity.” We know this because “we can observe genome reorganization in real time and relate what cells do now to what the DNA record tells us has happened over the course of evolution.”

So what is it microbiologists have found?

Genomic innovations occur at many different levels of complexity. These levels cover the entire range of DNA modifications: from single nucleotide substitutions, to short strings of nucleotides comprising regulatory signals, to longer polynucleotide strings encoding functional regions (“domains”) of protein molecules, through larger DNA segments encoding entire RNA or protein molecules, and finally extending to complexes of multiple coding segments and their attendant control regions.

In a surprisingly large number of cases, genome analysis tells us that reorganization events have comprised whole genomes. Because genome evolution is multilevel, amplifying, and combinatorial in nature, the end results are complex hierarchical structures with characteristic system architectures.

Genomes are sophisticated data storage organelles integrated into the cellular and multicellular life cycles of each distinct organism. Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations. (emphasis added)

If you didn’t follow all of that, here is the bottom line. Genetic changes in organisms are far more complex, multilevel, and systems oriented than previously thought. So what does this say about the standard Darwinian view of evolution as the gradual accumulation of random point changes in the genome over long periods of time? Shapiro explains that

the advent of molecular genetics and genome sequencing was a major step forward in evolutionary science. Examining the DNA record made it possible to subject traditional evolution theories to rigorous empirical testing. Do the sequences of contemporary genomes fit the predictions of change by “numerous, successive, slight variations,” as Darwin stated, or do they contain evidence of other, more abrupt processes, as numerous other thinkers had asserted?

The data are overwhelmingly in favor of the saltationist school that postulated major genomic changes at key moments in evolution. Only by restricting their analyses to certain classes of genomic DNA, such as homologous protein coding sequences, can conventional evolutionists apply their gradualist models. Moreover, we will see from genome sequencing that protein evolution itself often proceeds in relatively large steps. Contrary to the views of Linnaeus and Darwin, nature does indeed make leaps, and we now have molecular evidence of how some leaps occurred. (emphasis added)

One of the central dogmas of evolution, that change occurs by “numerous, successive, slight variations,” is wrong, according to Shapiro. Intelligent design proponents have been making this same argument for decades, but it seems that they now have company. I have no idea where this will all end up, but the ne0-Darwinian edifice continues to crack.

Evolution

Is There Any Scientific Controversy Over Darwinian Evolution? Part 1

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Post Author: Bill Pratt

I am told again and again by blog commenters that there is absolutely no controversy over any aspects of Darwinian evolution among those who study biology in the scientific community.  Here is a typical quote from a recent commenter, who was speaking about the pro-intelligent design Discovery Institute’s advocacy of teaching the controversy over certain aspects of evolution:

There is no scientific controversy. None. Not one bit. At all. This is purely a religiously motivated, and intentionally manufactured one, to appear as a scientific controversy. But appearances can be deceiving, especially when it is done intentionally to try to create controversy where none exists in scientific terms, one that does not match up to the evidence science has revealed from the reality we share.

But this is simply not true.  There is plenty of controversy in the world of evolutionary biology.  You just have to read.

I thought it would be helpful to point out just one prominent biologist’s disagreement with the standard evolutionary account.  His name is James Shapiro and he is a molecular biologist at the University of Chicago.  A pro-ID scholar, William Dembski, wrote a review of Shapiro’s latest book, Evolution: A View from the 21st Century, where he carefully describes Shapiro’s disagreement with the standard account.

Dembski starts by quoting evolutionary geneticist Jerry Coyne, who gives a succinct definition of evolution:

There is only one going theory of evolution, and it is this: organisms evolved gradually over time and split into different species, and the main engine of evolutionary change was natural selection.  Sure, some details of these processes are unsettled, but there is no argument among biologists about the main claims . . .  While mutations occur by chance, natural selection, which builds complex bodies by saving the most adaptive mutations, emphatically does not.  Like all species, man is a product of both chance and lawfulness.

Dembski continues:

Coyne here depicts the form of Darwinism that currently reigns, what is called the neo-Darwinian synthesis, which combines classical Darwinism (which holds to universal common ancestry, evolutionary gradualism, and natural selection) with modern genetic theory (which locates the source of heritable variation in genetic mutations, i.e., writing errors in DNA).

So, if this is the standard view of evolution, and there is no controversy over it, then we should expect Shapiro to agree with his colleague, right?  Wrong.  According to Dembski,

Of all these elements, Shapiro only subscribes to one, namely, universal common ancestry, or common descent, the claim that all organisms trace their lineage to a common ancestor (thus making all organisms alive today cousins). On every other point, Shapiro demurs.

Read that again.  Shapiro only agrees with common descent and disagrees with the rest of Coyne’s description of evolution.

Thus, when it comes to the claim that evolution proceeds gradually, Shapiro writes (p. 89): “Do the sequences of contemporary genomes fit the predictions of change by ‘numerous, successive slight variations,’ as Darwin stated, or do they contain evidence of other, more abrupt processes…? The data are overwhelmingly in favor of the saltationist school that postulated major genomic changes at key moments in evolution.”

If Shapiro simply left matters there, however, he might align himself with proponents of punctuated equilibrium who, keeping faith as much as possible with neo-Darwinism, see the principal source of biological variation in genetic copying errors, otherwise known as “mutations.”  But Shapiro rejects  this view as well.  For him, variation, which is always the creative potential of any evolutionary theory (no variation, no evolution), is not a random affair at all.  Rather, organisms intelligently control their variation and thereby facilitate the evolutionary process.

Shapiro writes (143): “Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth, and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities.  Cells are built to evolve; they have the ability to alter their hereditary characteristics rapidly through well-described natural genetic engineering and epigenetic processes as well as cell mergers.”

Dembski then concisely summarizes Shapiro’s view of evolution:

Organisms behave purposefully.  They evolve themselves.  They do this by intentionally modifying their own DNA.  Within neo-Darwinism, DNA is a read-only memory subject to occasional copying errors.  For Shapiro, DNA is a read-write memory, with the organism itself deciding when and where to modify its DNA.

Enough said, I think.  Shapiro differs dramatically from evolutionary orthodoxy.  He is representative of the active debate that is occurring among scientists who study evolution.  Why should these differing views not be openly discussed?  Why am I told that there is no controversy when there clearly is?  Let’s just admit that there are scientific debates within the evolutionary community, instead of pretending they don’t exist.