Tag Archives: Evolution

Commentary

Protein binding: by chance or intelligent design?

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Dr. Fazale Rana has this interesting post up on protein binding at Reasons to Believe.

Excerpt:

Nobody likes getting the flu. In fact, the influenza virus represents a serious health challenge. For most people it causes a few days of misery, but tragically for others, it takes their lives.

Biomedical researchers are looking for ways to develop therapies against the strains of the influenza virus that avoid destruction by the immune system or fail to respond to antiviral drugs. Recently scientists from the University of Washington and The Scripps Institute made progress toward this end. They designed novel proteins from scratch that bind to the stem region of hemagglutinin, a viral protein that plays a central role in the infection process.1 The hope is that the new proteins will have therapeutic use and also help with diagnosis.

This advance has obvious biomedical importance. It also contributes toward understanding the fundamental nature of protein-protein interactions (PPIs), and with this insight comes powerful new evidence that life stems from a Creator.

Often, in order to carry out their function, proteins must interact and bind in a highly specific manner with other proteins. These PPIs are selective. If the wrong proteins bind to each other, the interaction is of no use to the cell.

A large and varied population of proteins crowds the cell’s interior. Even the simplest bacterium harbors several thousand different types of proteins, along with numerous copies of the other biomolecules inside it. The jam-packed environment complicates things. Proteins are more likely to encounter the “wrong” partners than the ones they are designed to interact with.

Biochemists are currently working to understand the specificity of PPIs and how proteins avoid unintended interactions. As it turns out, protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions. Recent work by Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also designed carefully.

In other words, protein structure and concentrations have to be precisely regulated to promote the PPIs critical for life.

The rest of the article talks about all the intricate and cutting-edge engineering and computation done by the scientists to create a situation where the proteins could bind, and then ends with this:

When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:

…cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2

If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?

If you have to involve human intelligence to this degree, then I think that the best explanation is intelligent design.

Commentary

Paul Chien interviewed on the Cambrian era fossils

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Cambrian Explosion
Cambrian era fossils: Theory versus Data

From Leadership University. (H/T The Poached Egg)

Excerpt:

Dr. Paul Chien, chairman of the biology department at the University of San Francisco, recently accepted a unique invitation to travel to China to study fossils of the Cambrian era. What Chien found at the Chengjiang site, and what he has since learned about the Cambrian fauna, has changed the focus of his career. Today, Chien concentrates on further exploring and promoting the mysteries of the Cambrian explosion of life. Subsequently, Chien possesses the largest collection of Chinese Cambrian fossils in North America.

Chien attended Mere Creation, a conference last November sponsored by Christian Leadership, which was featured in the previous Real Issue. The following is an interview with Paul Chien.

RI: Dr. Chien, what is your interest in the evolution/creation debate?

Chien: Even before I became a Christian, I had doubts about evolution. During my college years I was really interested in finding answers, but I got very little help. For a while I lost interest because I thought, one way or the other, it wasn’t very important. But since I started teaching, many people ask me about that. In fact, I often speak at churches and youth groups and conferences, and I have been forced back to that question; it’s pretty much my hobby now.

RI: Until recently, you have focused on the effects of pollution on marine organisms. How then did you come to study the Cambrian “explosion of Life”?

Chien: In studying marine organisms, and mainly the invertebrate groups, I have a clear vision of the distinct characteristics of each phyla. The theory of evolution never [seemed to] apply well in my field of marine invertebrates. When the news broke concerning [the discovery of] an explosion of animal life, it really excited me because that [had been] my position for many years. Also, Phil Johnson’s chapter on fossils [Darwin on Trial, Intervarsity Press, 1991] really ignited my interest in that area.

When an opportunity came up to talk with Chinese paleontologists and to visit them and the original site of fossil discovery, it became something I had to do. So last March I organized an international group to make a visit there.

RI: So is the Chengjiang site a primary site for the Cambrian explosion?

Chien: Yes, it’s the site of the first marine animal found in the early Cambrian times we don’t count micro-organisms as animals.

RI: Are there other places in the world where you find the same organisms?

Chien: In some ways there are similarities between the China site and the other famous site, the Burgess Shale fauna in Canada. But it turns out that the China site is much older, and the preservation of the specimens is much, much finer. Even nerves, internal organs and other details can be seen that are not present in fossils in any other place.

RI: And I suppose many of these are probably soft-tissue marine-type animals?

Chien: Yes, including jellyfish-like organisms. They can even see water ducts in the jellyfish. They are all marine. That part of western China was under a shallow sea at the time.

RI: As you became more interested in this and discovered more about it, did you find it really was an “explosion of life”?

Chien: Yes. A simple way of putting it is that currently we have about 38 phyla of different groups of animals, but the total number of phyla discovered during that period of time (including those in China, Canada, and elsewhere) adds up to over 50 phyla. That means [there are] more phyla in the very, very beginning, where we found the first fossils [of animal life], than exist now.

Stephen J. Gould, [a Harvard University evolutionary biologist], has referred to this as the reverse cone of diversity. The theory of evolution implies that things get more and more complex and get more and more diverse from one single origin. But the whole thing turns out to be reversed we have more diverse groups in the very beginning, and in fact more and more of them die off over time, and we have less and less now.

RI: What information is the public hearing or not hearing about the Cambrian explosion?

Chien: The general impression people get is that we began with micro-organisms, then came lowly animals that don’t amount to much, and then came the birds, mammals and man. Scientists were looking at a very small branch of the whole animal kingdom, and they saw more complexity and advanced features in that group. But it turns out that this concept does not apply to the entire spectrum of animals or to the appearance or creation of different groups. Take all the different body plans of roundworms, flatworms, coral, jellyfish and whatever all those appeared at the very first instant.

Most textbooks will show a live tree of evolution with the groups evolving through a long period of time. If you take that tree and chop off 99 percent of it, [what is left] is closer to reality; it’s the true beginning of every group of animals, all represented at the very beginning.

Since the Cambrian period, we have only die-off and no new groups coming about, ever. There’s only one little exception cited the group known as bryozoans, which are found in the fossil record a little later. However, most people think we just haven’t found it yet; that group was probably also present in the Cambrian explosion.

Also, the animal explosion caught people’s attention when the Chinese confirmed they found a genus now called Yunnanzoon that was present in the very beginning. This genus is considered a chordate, and the phylum Chordata includes fish, mammals and man. An evolutionist would say the ancestor of humans was present then. Looked at more objectively, you could say the most complex animal group, the chordates, were represented at the beginning, and they did not go through a slow gradual evolution to become a chordate.

Someone posted an interesting documentary on Youtube about the Cambrian explosion.

Leadership University  is run by CLM, and features solid scholarship on a wide range of issues, including science.

News

How should Michele Bachmann answer the evolution vs intelligent design question?

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From ID proponents Jay Richards and David Klinghoffer. (H/T Stephen C. Meyer)

Excerpt:

Rep. Michele Bachmann is the latest to get pulled to the side of the road, lights flashing in her rear-view mirror. Talking with reporters in New Orleans following last week’s Republican Leadership Conference, she said “I support intelligent design,” referring to the theory that nature gives scientific evidence of purpose and design.

She continued: “What I support is putting all science on the table and then letting students decide. I don’t think it’s a good idea for government to come down on one side of a scientific issue or another, when there is reasonable doubt on both sides.”

Government neutrality would be welcome, as Bachmann rightly notes. But unfortunately the candidate’s statement generated headlines (“Bachmann: Schools should teach intelligent design,” as CNN.com summarized) that made her sound like she was ready to go a lot further than the intelligent design (ID) movement, which merely advocates that Darwinian theory’s weaknesses be taught along with its strengths. Allowing teachers to discuss ID in class would be much more appropriate and advisable than requiring them to do so.

[…]Fortunately, there’s an easy way to answer that takes account of the dilemma. Asked about evolution, here’s what Michele Bachmann, Tim Pawlenty, or Chris Christie could have said:

“Life has a very long history and things change over time. However, I don’t think living creatures are nothing but the product of a purposeless Darwinian process. I support teaching all about evolution, including the scientific evidence offered against it.”

Dogmatic neo-Darwinians won’t like that answer (they admit of no scientific arguments against their theory, unlike in any other area of scientific inquiry). But some other scientists will be fine with it, and, according to  Zogby polling data, so will the 80 percent of Americans who favor allowing students and teachers to discuss evolutionary theory’s strengths and weaknesses.

Such a formulation, true to the scientific evidence and to the Constitution, would also be devilishly hard for rival candidates to disagree with. Campaign staff and advisors would do well to commit something like it to memory.

I actually thought Michele’s answer was fine, but the suggested answer is better. If Michele Bachmann is picking a science adviser, either Stephen C. Meyer or Jay Richards would be a good choice. Pick someone with experience.