SCIENCE Questions: What Determines Species Diversity?

 
"What Determines Species Diversity?" is one of the top 25 questions from the 125th anniversary issue of Science magazine [Science, July 1, 2005]. The complete reference is ...

Pennisi, Elizabeth (2005) What Determines Species Diversity? Science 309: 90. [Text] [PDF]

Elizabeth Pennisi is a news writer for Science magazine. She has been publishing articles there for at least ten years. She had previously written about genes and genomes, including earlier articles about the number of genes in the human genome and one of the other top 25 Science questions [Why Do Humans Have So Few Genes?]

The question is poorly phrased because it's really about speciation.

Understanding what shapes diversity will require a major interdisciplinary effort, involving paleontological interpretation, field studies, laboratory experimentation, genomic comparisons, and effective statistical analyses. A few exhaustive inventories, such as the United Nations' Millennium Project and an around-the-world assessment of genes from marine microbes, should improve baseline data, but they will barely scratch the surface. Models that predict when one species will split into two will help. And an emerging discipline called evo-devo is probing how genes involved in development contribute to evolution. Together, these efforts will go a long way toward clarifying the history of life.

Paleontologists have already made headway in tracking the expansion and contraction of the ranges of various organisms over the millennia. They are finding that geographic distribution plays a key role in speciation. Future studies should continue to reveal large-scale patterns of distribution and perhaps shed more light on the origins of mass extinctions and the effects of these catastrophes on the evolution of new species.

This question is also related to a more fundamental question; namely, what is a species?

This certainly counts as one of the top questions in biology. If we ask it in the form "What causes speciation?" then it gets us into a discussion about punctuated equilibria, founder effects and all kinds of other controversial problems. It also brings up the issue of the role of natural selection and environment in speciation. While there may not be anything new to discover, there are many open questions concerning the mechanisms of speciation. Does sympatric speciation happen, for example?

There are many who think that natural selection plays only a minor role in most speciation events and there are many who think that environmental change is not correlated with speciation [Adaptation and Accident in PNAS, Evolution of Mammals].

Protein Turnover

 
One might assume that only growing or reproducing cells would require new protein molecules—and therefore a supply of amino acids—but this is not the case. Proteins are continually synthesized and degraded in all cells, a process called turnover. Individual proteins turn over at different rates. Their half-lives can vary from a few minutes to several weeks but the half-life of a given protein in different organs and species is generally similar. Rapid protein turnover ensures that some regulatory proteins are degraded so that the cell can respond to constantly changing conditions. Such proteins have evolved to be relatively unstable. The rate of hydrolysis of a protein can be inversely related to the stability of its tertiary structure—misfolded and unfolded proteins are quickly degraded.

In eukaryotic cells, some proteins are degraded to amino acids in the lysosomes. In these cases, vesicles containing material to be destroyed fuse with lysosomes, and various lysosomal proteases hydrolyze the engulfed proteins. The lysosomal enzymes have broad substrate specificities, so all the trapped proteins are extensively degraded.

Some proteins have very short half-lives because they are specifically targeted for degradation. Abnormal proteins are also selectively hydrolyzed. The pathway for the selective hydrolysis of these proteins in eukaryotic cells requires the protein ubiquitin. Ubiquitin is Monday's Molecule #29. It is a small, highly conserved protein of about 76 amino acid residues.

Side-chain amino groups of lysine residues in the target protein are covalently linked to the C-terminus of ubiquitin in a complex pathway that involves ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin-protein ligase (E3). This pathway is coupled to ATP hydrolysis—one ATP molecule is hydroylzed for every ubiquitin molecule attached to the target protein. The ubiquitinated protein is hydrolyzed to peptides by the action of a large multiprotein complex called the proteasome (or proteosome). This process occurs in both the cytosol and the nucleus.

Other proteases catalyze hydrolysis of the resulting peptides. ATP is required to assemble the proteasome and to hydrolyze the ubiquitinated protein. Before this pathway was discovered there was no explanation for the surprising observation that the degradation of many proteins requires ATP.


Adapted from Horton et al. Principles of Biochemistry 4th edition
©Laurence A. Moran and Pearson/Prentice Hall

SCIENCE Questions: How Does a Single Somatic Cell Become a Whole Plant?

 
"How Does a Single Somatic Cell Become a Whole Plant?" is one of the top 25 questions from the 125th anniversary issue of Science magazine [Science, July 1, 2005]. The complete reference is ...

Vogel, Gretchen (2005) How Does a Single Somatic Cell Become a Whole Plant? 309: 86.
[Text] [PDF]

Gretchen Vogel is a contributing correspondent for Science magazine. She is based in Berlin.

This question is really about developmental biology. It's closely related to the two questions that immediately precedes it in the journal: How Can a Skin Cell Become a Nerve Cell?, and What Controls Organ Regeneration?. For some reason the editors of Science seem to think that there's a fundamental difference between this question and the other two. Perhaps they think that plants control gene expression by a very different process?

The totipotency of plant cells was demonstrated half a century ago as noted in the article.

Nearly 50 years ago, scientists learned that they could coax carrot cells to undergo such embryogenesis in the lab. Since then, people have used so-called somatic embryogenesis to propagate dozens of species, including coffee, magnolias, mangos, and roses. A Canadian company has planted entire forests of fir trees that started life in tissue culture. But like researchers who clone animals (see p. 85), plant scientists understand little about what actually controls the process. The search for answers might shed light on how cells' fates become fixed during development, and how plants manage to retain such flexibility.

I really don't think it's correct to say that "plant scientists understand little about what actually controls the process." Furthermore, even if there are lots of details to be worked out, I see no indication that there's some mysterious unknown process behind plant development.

This is not a fundamental question.

bio::blogs #11

 
The 11th edition of bio::blogs, a carnival on bioinformatics, has been published at nodalpoint.org [Bio::Blogs #11].

A special edition of highlights can be found at Bioinformatics Zen [Bio::blogs 11 - special edition].

Did Dinosaurs Have Feathers?

 
An article on the National Geographic website addresses an issue in the evolution of birds ["Feathered" Dinosaur Was Bald, Not Bird Ancestor, Controversial Study Says].

The article deals with a recent report by a group at the University of KwaZulu-Natal in South Africa; University of North Carolina (Chapel Hill); and the Chinese Academy of Sciences, in Beijing. The paper was published in the journal Proceedings of the Royal Society B. The authors claim that the "feathers" seen on recent dinosaur fossils are not feathers at all but collagen fibers. This is a minority opinion and the reason why I mention the article is to point out how good science writing can put things in context. Here's an example,

Lingham-Soliar and colleagues' results support the arguments of a small but highly vocal group of scientists who say there's no evidence of dinosaurs ever having feathers.

"The existence of protofeathers in these dinosaurs was considered critical evidence that birds were derived from dinosaurs," said study co-author Alan Feduccia, a bird evolution expert at the University of North Carolina at Chapel Hill.

"What we have shown is that there's absolutely no evidence whatsoever that protofeathers existed in dinosaurs, period."

But the majority of scientists in the field are unconvinced.

The article then goes on to quote from a number of scientists who disagree with the findings of the South African group.

"These people have been flogging the same horse for a long time," said Kevin Padian, curator of the University of California Museum of Paleontology.

"It is appalling that Proceedings B chose to publish this nonsense."

We need more of this kind of reporting.

Lingham-Soliar, T., Feduccia, A., and Wang, X. (2007) A new Chinese specimen indicates that ‘protofeathers’ in the Early Cretaceous theropod dinosaur Sinosauropteryx are degraded collagen fibres. Proc. Roy. Soc. B: published online Wednesday, May 23, 2007

Monday's Molecule #29

 

Today's molecule is my first example of a protein. I've given you two different views of the molecule showing most of it as a ribbon model. A small stretch of the polypeptide is displayed as a stick model. You have enough information to identify the protein provided you have taken the appropriate courses in high school or college. All we need is the name of the protein but if you can identify the species and the PDB file that would be an impressive feat of detective work.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate(s). This one is an direct connection. Once you have identified the molecule the Nobel Laureate(s) are obvious.

The reward (free lunch) goes to the person who correctly identifies both the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are no ineligible candidates for this Wednesday's reward since recent winners have declined the prize on the grounds that they live in another country and can't make it for lunch on Thursday. There was no winner last week although several people were close.

Comments will be blocked for 24 hours. Comments are now open.

Mendel's Garden #15

 
Visit The Daily Transcript for your complete list of summer reading, courtesy of Gregor Mendel Mendel's Garden #15 - Summer Reading Edition]. Of course you'll already know about what causes wrinkled peas because you've been reading Sandwalk. Don't let that put you off. There's plenty of other good stuff there.

Take the Carnegie Mellon University Survey on Ethical Standards

 
This is a survey on ethics developed by workers at Carnegie Mellon University for readers of the New York Times [Survey on Ethical Standards]. We can take the survey thanks to John Tierney and his blog TierneyLab: Putting Ideas in Science to the Test [Test Your Ethics (or Lack Thereof)].

The nice thing about this survey is that you can instantly see how you answered the questions relative to everyone else who took the survey. I was very pleasantly surprised at some of the responses. If you take the survey, make sure you do it alone and in a private place. You must answer all questions honestly and you may not want friends or relatives to know your answers. Try it, and then see how everyone else answered the questions.

I've been trying to stimulate some discussion about ethics without much success [Ethical Issues in Biochemistry]. There's a growing tendency in science education to include classes on ethics but nobody seems to be able to define ethics in a way that makes sense to me. What, exactly, is an ethical issue? [see, Ethics on Wikipedia] Take the survey to see if your sense of "ethics" agrees with others.

The other problem is how do you teach ethics to undergraduate science students? What are the basic principles of ethical reasoning? Is ethical relativism a valid philosophy or are there some "rules" that every undergraduate should memorize? [see, Moral Relativism on Wikipedia] I've encountered scientists who claim that we need to teach students that ethical relativism is a failed philosophy and there really is a "right" and a "wrong."

Here's a question that's not on the survey. Does whether or not you would have your genome sequenced [Sequencing Jim Watson] count as an ethical question? I don't think so. It's a question about personal preferences and the answer depends very much on how you feel personally about issues such as privacy. This isn't "ethics" as far as I'm concerned.

Sequencing Jim Watson

 
Jim Watson has just become the first person to have his complete genome sequenced. Craig Venter's genome sequence is not far behind.

Watson's genome was sequenced at the Baylor College of Medicine's sequencing center in collaboration with 454 Life Sciences, a private company that developed some new sequencing techniques. Apparently, the sequence was completed in two months at a cost of $1,000,000. Watson received the results on two DVDs. He promises to deposit it in the public database except for the sequence of his apolipoprotein E gene. He does not want to know which allele he carries because some of them are associated with Alzeimer's disease.

Here's the question for the day. Would you want to know the sequence of your genome if all you had to do was supply a small blood sample to get it? What are the implications? Do your children have a say if you intend to release your genome sequence into the public domain.

I can tell you that I would not do it. Perhaps the older I get the more I'm inclined not to care which alleles I carry but I would always be concerned about what effect it might have on my children—although that may be an unrealistic concern since they seem to have gotten all their good genes from me!

Watson is 79 years old and has two grown children.

[Genome of DNA discoverer is deciphered]
[Nobel Laureate James Watson Receives Personal Genome]
[Project Jim, celebrity sequencing, and the divine right of geneticists]

Ethical Issues in Biochemistry

 
The American Society for Biochemistry and Molecular Biology (ASBMB) has established guidelines for undergraduate programs in biochemistry and molecular biology (Voet et al., 2003). The society has now received a grant from the Teagle Foundation to access the relationship between the goals of a major in biochemistry and those of a liberal education (Wolfson, 2007).

Here's a list of skills that biochemistry and molecular biology undergraduates should obtain by the time they graduate.

• Understanding of the fundamentals of chemistry and biology and the key principles of biochemistry and molecular biology.
• Awareness of the major issues at the forefront of the discipline.
• Ability to assess primary papers critically.
• Good quantitative skills such as the ability to accurately and reproducibly prepare reagents for experiments.
• Ability to dissect a problem into its key features.
• Ability to design experiments and understand the limitations of what the experimental approach can and cannot tell you.
• Ability to interpret experimental data and identify consistent and inconsistent components.
• Ability to design follow-up experiments.
• Ability to work safely and effectively in a laboratory.
• Awareness of the available resources and how to use them.
• Ability to use computers as information and research tools.
• Ability to collaborate with other researchers.
• Ability to use oral, written, and visual presentations to present their work to both a science-literate and a science-non-literate audience.
• Ability to think in an integrated manner and look at problems from different perspectives.
• Awareness of the ethical issues in the molecular life sciences.

This is your chance to comment on this list. I'll make sure your comments are passed along to Professor Wolfson so she can incorporate them into the study. I don't necessarily support everything on the list.

I'd like to start with the last one "Awareness of the ethical issues in the molecular life sciences." How important is this in a biochemistry/molecular biology undergraduate program? Who do you think should teach it? What kind of issues should we cover? Should there be some instruction on ethics philosophy?

Wolfson, A.J. (2007) Biochemistry and Undergraduate Liberal Education. Biochem. Mol. Biol. Educ. 35: 167-168.

Voet, J.G., Bell, E., Boyer, R., Boyle, J., O'Leary, M. and Zimmerman, J.K. (2003) Recommended curriculum for a program in biochemistry and molecular biology. Biochem. Mol. Biol. Educ. 31: 161-162.

Biochemisty and Molecular Biology Education

 
Biochemistry and Molecular Biology Education (BAMBED) is a journal published by Wiley on behalf of the International Union of Biochemistry and Molecular Biology. The journal is linked to the American Society for Biochemistry and Molecular Biology.

BAMBED publishes papers about education and education issues. The Editors-in-Chief are Donald Voet and Judith Voet. I happen to be on the editorial board and that's why I'm blogging about this journal. More people need to know about it.

Here are some of the articles in this month's issue to give you an idea of the sorts of things that educators are concerned about.

Adele J. Wolfson Biochemistry and undergraduate liberal education (p 167-168)

Vicky Minderhout, Jennifer Loertscher Lecture-free biochemistry: A Process Oriented Guided Inquiry Approach (p 172-180)

Brian J. Rybarczyk, Antonio T. Baines, Mitch McVey, Joseph T. Thompson, Heather Wilkins A case-based approach increases student learning outcomes and comprehension of cellular respiration concepts (p 181-186)

James K. Zimmerman Proper reporting of results (p 198)

Lauren Walsh, Elizabeth Shaker, Elizabeth A. De Stasio Using restriction mapping to teach basic skills in the molecular biology lab (p 199-205)

Harold B. White Commentary: What do students say about problem-based learning? (p 211-212)

Matthew Nisbet and Chris Mooney Video on Framing Science

 
Chris Mooney has challenged me to respond to a video (see below the fold) of a talk that he and Matt Nisbet gave on framing. Over on his blog, Chris criticizes PZ Myers who couldn't sit through the whole hour [PZ, You Can Do Better Than This....]. Neither could I, but at least I got to the 50 minute mark which was more than twice as far as PZ.

Chris and Matt believe their talk is much more detailed than their short paper in Science or any of their other articles. They think that with this longer version they will have answered the objections raised by a number of scientists. This is quite in line with the position they have taken over the past few months. Their main defense has been to proclaim that we just don't understand framing and that's why we don't appreciate their opinions. That defense has the tremendous advantage (for them) of avoiding having to deal with any of the objections that have been raised. It's probably a good example of framing on their part.

Here's how Chris Mooney puts it today in addressing PZ,

So, c'mon, PZ. You've ripped the "framing science" concept based upon brief essay-style presentations of it. Now we've gone all out and produced a much more thorough presentation--one that covers, in depth, the concept of framing; evolution; stem cell research; global warming; hurricanes; and then closes by presenting policy solutions--and you won't engage.

I'm disappointed by this, but I also know you're a thoughtful guy. So I'll happily give you the benefit of the doubt here and ask you again to engage with our arguments as we have now chosen--comprehensively--to present them.

Notice how this works. PZ, and others, have already explained why they have a problem with framing science. Matt and Chris didn't listen. Now they want everyone to explain it to them once again just because they've produced an extended version of their opinions.

Well, Chris, I hate to break it to you, but there's nothing new in the video. It's just the same old fluffy rhetoric that we've seen before. I watched for 50 minutes and you never once addressed the main objections that you heard from many scientists. The ball was clearly in your court and you dropped it. You had one hour to engage our arguments and show that you were listening but you didn't do that. Why?

Have you forgotten the problem? You claim to be talking about "science education" and "science communication" but you are actually talking about politics. Scientists do not deliberately "frame" science. They tell it like it is. On the other hand, if you are trying to score political points or advocate policy change then you can use any trick in the book if you think you can get away with it. The fact that some of these political battles might be related to science is interesting but almost irrelevant. You could make exactly the same case for framing if you were engaging in political battles over the constitution, economic policy, or the war in Iraq.

As far as I'm concerned you and Matt are doing serious harm to science. You are strongly implying that it's okay to spin the science in order to achieve a political objective. Not only are you implying that, you are criticizing scientists for not learning how to spin frame science properly. One thing you could easily do to fix this problem would be to stop talking about framing science communication and substitute talk about framing political debates concerning scientific topics.

The other problem with your talk is that you continue to criticize Richard Dawkins for raising problems about religion and promoting atheism. Fine, that's your opinion and you're stuck with it. But you know damn well that many of us think you are way off base on that one. You've heard this point of view many times but you never addressed it in your talk. Why couldn't you have discussed the other point of view; the one that says arguments about religion are not the same as arguments about science? I would have had much more respect for you if you had showed me that you were listening to your opponents. At the very least you could have mentioned the difference between long-term goals and short-term goals and explained why you think Dawkins should sacrifice his long-term goal in favor of your short-term goal.

Finally, there's a problem that only concerns me and other non-Americans. Everything you say is "framed" as an American problem. You're talking about the American public, American politics, and American journalism. Your solutions only apply in that context. Your chosen frame does not resonate with me. Maybe you don't care about scientists in Canada or Europe (I'm sure you don't) but when you're broadcasting to the entire world don't be surprised if some of us don't care about you either.

You do realize, don't you, that Richard Dawkins lives in the United Kingdom? Do you understand that in terms of political debates, different spins will be adopted by people in different countries? It's just not possible for you and Matt to impose your American values on scientists in Japan, India, and Europe. But since we now live in a global village these foreigners are going to be heard in your country as well. How do you propose to maintain discipline under those circumstances? You are tying to herd cats, this strikes me as more than a little naïve.

For the benefit of readers, here's the video. The part about how to frame a political debate on evolution and creation can be found about 22 minutes into the talk at the 48 minute marker. (The timer starts at 70 minutes and counts down.)

The Bora Zivkovic Rules of Science Communication

Bora Zivkovic ("Coturnix") has posted on the Bloom and Weisberg article and on the issue of Do You Trust Scientists?. Naturally Bora has some ideas on this and (surprise) they involve framing.

Since he specifically mentions me [More than just Resistance to Science], I thought I might as well respond.

That is why, Larry's protestations notwithstanding, we desparately need the advice of people whose job is to study communication. We have no idea how to talk to people with hierarchical worldviews and the phatic use of language and we better listen and be prepared to learn.

Name some names. Show me these mythical communications experts who are doing such a good job of communicating science to the general public. Where in the world did you come up with this ridiculous idea that scientists have no idea how to talk to the average person?

All the examples that Larry points out - teaching science majors in college, talking to other scientists, writing popular science books, writing science blogs - are aimed at the audience that already is rational and uses language to get and impart information. It just does not work in persuasion and education of the irrational folk. The way to frame the science is completely different.

Bull. The way to talk to irrational people is not to get down in the gutter with them and behave irrationally. How in the world do you expect people to trust you, Bora, if you abandon the core principles of science?

So, what do we do?

Phase 1 is to attain authority (that is why science reporters will not do for this - it has to be scientists themselves). In doing so, the scientists have to do more than just assert equal authority as the priest, sheriff and mayor. For a hierarchically-minded audience, the only way to rise in authority is for someone else's authority to diminish at the same time ("How can the UN tell MY President what to do?"). It is a ladder they think of and only one person or group can be at any single rung of it. Thus, scientists have to displace clergy, lawyers and politicians as sources of authority on scientific matters.

I agree with this. Scientists need to challenge religion since in the USA that's the dominant authority. The first step is to get their attention by making some noise. So far it's working.

How does one do this? When dealing with kids (and adults who have not yet made the change to a rational worldview), the only way is to appear to be 100% sure. This is not the audience that gets error-bars, confidence intervals, fine points of philosophy of science, and alternative hypotheses. You tell it how it is (even if inside you cringe, knowing that what you are saying is only 98% sure). You tell it with conviction. No need to lie. Just get out of the science-paper mindset. The studies mentioned in the Edge piece confirm this notion as well.

You do that and you've lost my respect. What do you get in return? You get the same kind of respect as politicians and everybody else who's prepared to sacrifice truth for spin. What you're advocating is not "framing," it's surrender.

"Truth" is something like "pregnancy." Something is either true or it is not true. There's no such thing as 98% true. That's just a polite word for a lie. "Spin" is another polite word for a lie and so, it appears, is "framing."

Phase 2 is to gain trust. As Sara Robinson explained in her series "Tunnels and Bridges" and "Cracks in the Wall" (both found in the sidebar here), this is a slow and gradual process. No looking down at people. Not calling them stupid or evil. Giving them a helping hand and encouragement. Perhaps promise an induction into a secret powerful society of scientists. Even if one makes small steps, reward them even if you do not like where they got in the process: smile when the individual moves form YEC to OEC, and again when he moves from OEC to IDC, and again when he moves from IDC to Theistic Evolution, and again when he moves from Theistic Evolution to a genocentric, hyperadaptationist form of naturalistic evolution and give them a damned PhD when they understand and accept the modern evolutionary theory.

Whatever. You do it your way and I'll do it my way. There's plenty of room for all kinds of personalities in this battle. For the time being I'm impressed with the Dawkins approach. People have been trying it your way for decades and look at what kind of success they've had in America.

For over a century, the creationists have been mocking, criticizing, and demeaning scientists from the pulpit, in books, on television and in newspapers. Not only do they call us stupid but evil as well. Guess what? That strategy has been working for them. It's time to fight back. Think of it in terms of attack adds if that makes you feel better. Except that our attack adds are truthful.

While phases 1 and 2 can, to some extent, be done simultaneously, Phase 3 can be attempted only once the person has already passed the first two phases. The Phase 3 is science education as we understand it. It can only be applied to the audience that is already rational and uses language for the exchange of information, not emotions. Actually understanding the world, not just taking your word for it (phases 1 and 2 are pretty much getting people to trust you on your word, not understanding any science yet) is something that we want them to achieve and traditional science education can do so. I am sure that Larry is really good at this phase, even though he refuses to acknowledge that the first two phases are necessary or even existent before a person can understand and accept what Larry is teaching.

Oh come on, Bora, I'm not nearly as stupid as you imagine. If the other phases are to establish trust and gain authority then I'm perfectly aware of the fact that these are important. Just because I think that your tactics will do the exact opposite does not mean that I reject the goal.

The problem is, you can't have it all. You can't expect to get "respect" by lying about science, or framing it in ways that are unacceptable to scientists, and then expect to turn around and teach good science. By the time you've spun your way to "respect" you lost the moral authority to teach.

Does Sandwalk Own Me?

 

25 %

My weblog owns 25 % of me.
Does your weblog own you?

[Hat Tip: Shalini]

Darwin and Design by Michael Ruse

 
In Darwin and Design Michael Ruse tackles a tough problem; namely "Does evolution have a purpose?" Unfortunately the correct answer is "no" but Ruse muddles, misdirects, and misunderstands so thoroughly that by the time you reach the end of the book you just want to throw it against the wall.

The main theme of the book is teleological thinking or the idea that things happen in order to achieve a goal. We are familiar with this way of thinking in religion. Ruse spends some time describing the history, culminating in the natural theology of William Paley.

Paley and others argued that the presence of design in nature demanded a God who was the designer. The teleological part of this argument is the recognition that designed species, especially humans, represent a clear goal that needs an explanation. Life has meaning and purpose, according to believers, and it is God who gave it to us.

A teleological argument, or argument from design, is an argument for the existence of God or a creator based on perceived evidence of order, purpose, design and/or direction in nature. The word "teleological" is derived from the Greek word telos, meaning end or purpose. Teleology is the supposition that there is purpose or directive principle in the works and processes of nature.
"Teleological Argument" WikipediaCharles Darwin explained how life could appear to be designed by invoking natural selection, thus removing God from the equation. Nevertheless, teleology remains an important part of science, according to Ruse, because nature is designed by natural selection. It is quite appropriate, he says, to argue from design (the eye for example) to cause (adaptation).

This then is the paradox to which Darwin and Design is directed. Darwin seems to have expelled design from biology, and yet we still go on using and seemingly needing this way of thinking. We still talk in terms appropriate to conscious intention, whether or not we believe in God. In biology we still use forward-looking language of a kind that would not be deemed appropriate in physics or chemistry. Why is this?

Ruse seems to be at his best when describing the history of philosophy—as long as that history pre-dates Charles Darwin. His book is worth reading if you want a good summary of the design argument up to 1859. From that point on things begin to fall apart because Ruse does not understand modern evolution and he does not understand the controversies over evolutionary theory that persist to this day. Consequently, all of his history from Darwin on is biased and wrong.

The essence of Ruse's argument is as follows. Life evolves by natural selection. This leads to species and characteristics that are well-adapted. These characteristics have the appearance of design because they are, in fact, designed by natural selection. Because we know that everything is an adaptation it's perfectly legitimate to look at a species or an organ and assume that it as been designed by natural selection. While this adaptationist program may seem teleological because it assumes a purpose, it is, in fact a very legitimate way to do biology because design is a fundamental part of biology.

There are times when one thinks that Michael Ruse must have slept through the last half of the twentieth century. Has he never heard of Gould & Lewontin and The spandrels of San Marco? Is he unaware of the controversy over the validity of the adaptationist program?

Yes and no. He's heard of the controversy but he just wasn't listening. Everyone else who has addressed this question recognizes that the Gould & Lewontin challenge is not going to go away. They attempt to deal with it—usually not very successfully.

To his credit, Ruse seems to have picked up on the rumors that something important was going on so he does mention the spandrels paper and the attack on the adaptationist program. It's right there on pages 234-239. Five pages on structural constraints as introduced by Gould & Lewontin in their famous 1979 paper. Structural constraints? Surely there's more to the argument than that? Yes, there is but Ruse can easily dismiss it,

The point is whether they [Gould & Lewontin] introduce a whole new dimension into the discussion, by showing that much in the organic world is fundamentally nonadaptive. Darwinians have failed to see this and still continue not to see it.

That's it. Ruse is blind to modern evolutionary theory and quite proud of it. According to Ruse everything is an adaptation and "Darwinism" and "evolution" are synonyms.

The rest of the five pages on Gould & Lewontin are no more enlightening. Lest you think I'm being too harsh on Ruse, I assure you I'm not. He really doesn't get it. There are two pages devoted to random genetic drift. Two pages! After acknowledging that drift can sometimes cause evolution he dismisses it out of hand with,

Over time, however, random drift would be expected to average out more smoothly than differences due to the ever-changing forces of selection. For this reason the hypothesis that most molecular difference is due to drift has not been well received. Time and time again, measurements have shown that molecular differences are not what we would expect were drift the sole or main cause of change. In fruit flies, we see how random drift was ruled out as a significant factor in changing levels of the Adh gene.(p. 201)

Having summarily dismissed all objections to the ubiquity of adaption, Ruse can defend the argument from design by invoking adaptation as the sole driving force of evolution. In a chapter on "Design as Metaphor" he outlines his version of the adaptationist program. It's not only appropriate to attribute design to living things but it's a very productive way of advancing scientific knowledge.

Organisms produced by natural selection, have adaptations, and these give the appearance of being designed. This is not a chance thing or a miracle. If organisms did not seem to be designed, they would not work and hence would not survive and reproduce. But organisms do work, they do seem to be designed, and hence the design metaphor, with all the values and forward-looking, causal perspective it entails, seems appropriate.(p. 276)

Critics of the adaptationist program—I am one—argue that it begs the question. When you see something in nature it is reasonable to assume that it arose by evolution. The question we want to answer is what kind of evolution gave rise to that particular characteristic?

Take the fact that some people can roll their tongue as a simple example. We know there is a genetic basis to tongue-rolling. Some people have the allele that allows it, and some don't. We want to know why tongue-rolling exists.

     Once you have the metaphor of design in play, then of course you can ask questions about borderline instances and extensions and so forth. The real question, though, is whether, in the first place, the metaphor itself is an appropriate one. The question is not whether metaphors should be used at all but whether the specific metaphor of design should be used to explain evolution.

     Darwinians argue strenuously that it must be used. Richard Dawkins speaks to precisely this issue, asking what job we expect an evolutionary theory to perform. ... Dawkins agrees with John Maynard Smith that the "main task of any theory of evolution is to explain adaptive complexity, i.e. to explain the same set of facts which Paley used as evidence of a Creator."
Michael Ruse p. 278If you are a modern evolutionary biologist then you are aware of several possibilities. It could be just an accident that has no great significance at all. Maybe tongue-rollers and non-tongue-rollers have an equal chance of leaving offspring and the alleles will be fixed or eliminated by random genetic drift. Or maybe one of these groups has a selective advantage. Maybe tongue-rollers are more successful at having children and that's why the allele persists in the population. Eventually everyone will be a tongue-roller because natural selection is operating.

If you are a committed adaptationist then you begin by assuming that the ability to roll your tongue is designed. Your task is then to explain how this design arose and you have only one choice—evolution by natural selection. Thus, your choice of the design metaphor has blinded you to the possibility that tongue-rolling may not be an adaptation at all. This is a very restrictive research program because the question pre-supposes the answer. In other words, by imposing design and purpose on the natural world—albeit natural and not divine purpose—Ruse and his colleagues are avoiding the very question they should be asking; namely, "is this an adaptation?" This bias leads to fanciful just-so stories as the adaptationists struggle to come up with imaginary ways of explaining the design that they think they see in nature.

Does Ruse have an answer to this objection? Yes he does,

The critic might respond that one has here a circular situation: Darwinians make searching for adaptation central to their program, and then when they find the adaptations they so fervently seek, they use them as support for Darwinism. But a better term than "circularity" might be "self-reinforcement." Darwinism is a successful theory—our scientific examples show that—and at the moment (and for the foreseeable future, whatever the qualifications) it is the only game in town, on its own merits. Fruit flies, dunnocks, dinosaurs, fig wasps—this is a theory on a roll. It has earned the right to set the agenda. (p. 280)

As far as I'm concerned this is dead wrong. Darwinism is not the only game in town and we've known that for almost fifty years. At the very least you have to consider fixation of alleles by random genetic drift. If this is how a character actually evolved then there is no design. The metaphor is inappropriate. The program is useless. (There are other non-Darwinian processes.)

The entire thrust of Ruse's argument for design and purpose in evolution is absolutely dependent on one critical assumption: that natural selection is the only significant mechanism of evolution. If this isn't true then his whole argument falls apart. It isn't true.

I accept Ruse's challenge when he says,

Of course, Lewontin and his school do not care for many of the findings of the adaptationists. But to say that we should not play the game at all, or that we should count all as equal, requires some persuasive arguments. Better than arguments would be examples. Let those who worry about explanatory adaptationism show their dunnnocks and dinosaurs and fig wasps. When they demonstrate that they can do science which explains and predicts without invoking adaptation even implicitly, then we can start taking their position seriously. (p. 281)

There are literally dozens of examples of non-adaptive evolution that have been widely discussed in the scientific literature. It is more than "silly" of Ruse to issue a challenge like this. It's just plain ignorant.

Scientists who study junk DNA, for example, are doing very legitimate science when they predict that junk DNA sequences will not be conserved between species. Scientists who study blood type in humans are doing real science when they test the null hypothesis by asking whether the alleles conform to the Hardy-Weinberg distribution. (They do, suggesting strongly that they are not under selection.) Scientists who study speciation in birds ask whether the founder effect is real. (It is, and this shows that morphological changes during speciation are not due to adaptation.) The late Stephen Jay Gould and his colleagues have done good science by developing theories of punctuated equilibria and species sorting without assuming that natural selection and adaptation are essential. Ruse needs to take their position seriously. Meanwhile Ruse has demonstrated that we don't need to take him seriously.

The entire field of molecular evolution is based largely on explanations and predictions that rely on random genetic drift of neutral alleles. As far as I know, the people who work in that field are good evolutionary biologists even though they don't assume design when constructing their phylogenies.

And lets not forget about one of Lewontin's favorite examples. The African rhinoceros has two horns while the Indian rhinoceros has only one. Why? If you accept the modern theory of evolution then your choices of explanation can range from adaptive to accidental. If you restrict yourself to Darwinism then you must assume design and your explanation has to invoke natural selection. Somehow you have to come up with ways to explain why African rhinos were better off with two horns while Indian rhinos were better off with only one.

Using the metaphor of design and purpose forces you to assume the answer to the very question you are asking. It forces you to reject known evolutionary mechanisms such as random genetic drift. This may be good philosophy but it's not good science.

Getting back to the title of the book. Is nature designed? Partly, but there are lots of things that don't look designed and are not the end product of natural selection. Our genome is a good example. It's more like a Rube Goldberg apparatus than a well-tuned machine. It is not particularly helpful to say that living things are designed, or even that they have the appearance of design. If we stop saying that everything is designed then we will be better prepared to consider other possibilities, like evolution by accident.