Evolution for Idiots

 
Here's a short video that has just been posted on The Panda's Thumb. You can read the comments over there or watch the video here. Let's make our own list of everything that's wrong with it. Sometimes I wonder whether these things help or hurt the cause of science education. Today I'm leaning towards "hurt."

Blood Clotting: Intrinsic Activity

 
Blood clotting is initiated by the extrinsic activity which is localized to the surfaces of tissue factor (TF) bearing cells. These cells are located at the site of injury [Blood Clotting: Extrinsic Activity and Platelet Activation]. The initial steps result in activation of some blood coagulation factors and activation of platelets.

The next step in coagulation requires an amplification of thrombin production so that clotting can proceed rapidly. The amplification stage is referred to as intrinsic activity, or the intrinsic pathway. These reactions take place on the surface of activated platelets. Activated platelets aggregate at the site of injury [Blood Clotting: Platelets].

The ultimate goal in the amplification stage is to create a prothrombinase activity on platelet surfaces. Prothrombinase will cleave prothrombin to make thrombin and thrombin is the enzyme that cuts fibrinogen to make fibrin for clot formation [Blood Clotting: The Basics]. The platelet prothrombinase activity is the same as the activity on TP-bearing cells: it’s formed from Xa and membrane-bound Va. The difference between the two pathways (extrinsic and intrinsic) is the way in which factor X (ten) is activated to form Xa. The platelet enzyme is called “tenase” (cleaves factor “ten”) and it’s formed from Factor VIIIa and Factor IXa.

The final steps are shown in the figure below. Large amounts of thrombin are generated and large amounts of fibrin are produced.


Tenase activity is formed when VIIIa binds to the platelet membrane. VIIIa is produced by thrombin cleavage of factor VIII in the extrinsic part of the pathway. Factor VIII is the factor that associates with von Willebrand factor (vWF). The most common hereditary bleeding disorder is caused by a deficiency of von Willebrand factor (von Willebrand diseases). In the absence of vWF, factor VIII is unstable and platelets cannot form the tenase enzyme. Hemophilia A is the X-linked form of hemophilia that was common in European royal families descending from Queen Victoria. It is caused by a deficiency of Factor VIII.

IXa, the active component of tenase, is produced when XIa cleaves the precursor factor IX. Deficiencies in factor IX cause hemophilia B. IX is another factor that contains a γ-carboxyglutamyl residue that chelates a Ca⁺⁺ ion.

A little bit of IXa is made in the extrinsic pathway but the major amplification on platelet cell surfaces requires XIa. The pathway leading to formation of XIa is shown on the left. HMWK stands for “high molecular weight kininogen.” It binds to and stabilizes XIa and kallikren.

Thanks to my colleague Marion Packham for answering some questions about platelets. I recommend the Hemostasis & Thrombosis chapter in Harper's Illustrated Biochemistry 27th ed. written by my colleagues Marg Rand and Bob Murray.

Devlin, T.H. (ed.) (2006) Textbook of Biochemistry with Clinical Correlations 6th ed., Wiley-Liss, Hoboken, N.J. (USA)

Rand, M.L. and Murray, R.K. (2006) Hemostasis & Thrombosis in Harper's Illustrated Biochemistry 27th ed., R.K. Murray, D.K. Granner, and V.W. Rodwell eds. McGraw Hill Lange, Toronto Canada.

Wolberg, A.S. (2007) Thrombin generation and fibrin clot structure. Blood Reviews Jan. 5 2007. [PubMed]

Blood Clotting: Extrinsic Activity and Platelet Activation

 
We've seen that blood clots are formed when fibrin molecules aggregate at the site of injury to form a fibrous clot. Fibrin is produced by cleaving the precursor fibrinogen. The enzyme that cuts the protein is a protease called thrombin [Blood Clotting: The Basics].

Thrombin is the active form of the protease enzyme. It is derived from a precursor called prothrombin and the production of thrombin at the site of injury requires an enzyme to cleave prothrombin. This enzyme is called prothrombinase. Like thrombin, prothrombinase is a protease only its substrate is prothrombin instead of fibrinogen.

Prothrombinase is a multisubunit enzyme composed of two different polypeptide chains. One of them is an activated form of Factor V (factor five) called FVa or just Va. The "a" signifies an activated form of a clotting factor. The other subunit of prothrombinase is an activated form of Factor X called FXa (activated factor ten). Xa plus Va together make the prothrombinase that cleaves prothrombin to make thrombin. This leads directly to blood clotting.

In order for this cascade to be initiated there has to be some trigger that leads to formation of prothrombinase (Xa + Va). This trigger has to be localized to the region where a blood vessel is damaged so that the blood clot forms at the right place. The initiation step is called the extrinsic activity.


The cells lining blood vessels contain a membrane protein called tissue factor (TF). It is sometimes referred to by its old name Factor III. TF is normally masked but it becomes exposed when the cells are damaged. Factor VII (VII) binds to exposed TF to form a protease that cleaves Factor X to Xa. Xa plus Va then cleaves prothrombin to thrombin and thrombin activates a number of other factors that will enhance the clotting. There is always a little bit of Va circulating in the blood stream and it binds to TF-bearing cells when the membrane is exposed.

VII is one of the proteins containing a γ carboxyglutamyl residue. This is a modification that requires vitamin K [Vitamin K, Nobel Laureates: Dam and Doisy]. The γ carboxyglutamyl residue binds to calcium ions (Ca⁺⁺). Calcium is an important cofactor in clot formation because there are several factors with γ-carboxyglutamyl resides. They must bind Ca⁺⁺ because the postive charges allow the proteins to interact with negatively charged (anionic) surfaces such as those that are exposed when membranes are disrupted. The binding to anionic molecules explains why heparin (Monday's Molecule #20) inhibits clotting but we'll get to that another day.

The important activation steps that are catalyzed by thrombin are the conversion of Factor VIII to VIIIa and Factor IX to IXa. These contribute to the activation of platelets as we will see in the next posting. Factor VIII circulates in blood plasma as a complex with von Willebrand factor (vWF) but upon cleavage of VIII to VIIIa vWF dissociates. As you can see from the diagram, the first thrombin that is formed also cleaves Factor V to Va and this greatly increases the concentration of Va, which bind to the TF-bearing cells. This, in turn, leads to more prothrombinase being produced and more thrombin—an example of positive feedback.

The VIIa/TF complex also cleaves Factor IX to IXa. This serves to stimulate activated platelets.

Thrombin will also cleave some fibrinogen to fibrin initiating clot formation. However, the rate of fibrin formation that results from extrinsic activity is not sufficient to support the formation of a large clot. An additional step called intrinsic activity is needed to amplify the production of thrombin. This requires active platelets.

Active platelets look very different from the inactive forms. The active versions have a much more irregular shape and they have many extensions. It is the active platelets that aggregate to form a plug at the site of injury and the enhanced clotting activities take place on the platelet membrane surfaces.


[The clotting pathways are modified versions of figures from Wolberg, 2007]

Blood Clotting: Platelets

 
Platelets are small bits of cells that aid in the formation of blood clots and help seal breaks in blood vessels.

They are formed by pinching off small bits of a large cell called a megakaryocyte. Megakaryocytes are found in bone marrow. The platelets contains mitochondria and cytoplasm but no nuclei.

Platelets have a number of enzymes and factors that promote wound healing and their membranes are studded with various receptors and factors that promote blood clotting at the site of injury. Normal blood has a very high concentration of platelets (200,000 per microliter) - this is the platelet count that's a common diagnostic test for many medical problems. Platelets have a half life of about ten days so they need to be continuously produced in the bone marrow.

When a blood vessel is injured a patch of endothelial cells are destroyed exposing the underlying collagen matrix. Platelets bind to collagen and then to each other leading to an aggregation of platelets and formation of a plug that stops the bleeding. The platelet plug also stimulates blood clotting at the site of injury because many of the factors that promote clotting are carried by platelets.

This process is shown in the electron micrograph on the right. The platelets are the small dark cell-like objects. Some of them have adhered to the collagen matrix on the far right and this stimulates other platelets to bind to the ones that first arrived at the lesion. A platelet plug is building.

These platelets will also become activated for formation of fibrin blood clots at this site. Many of the proteins on the cell surface will aid in generating thrombin from prothrombin. Thrombin cleaves fibrinogin to produce the clotting protein, fibrin [Blood Clotting: The Basics].

Gary Carlson has created a number of very impressive images of platelets. Click on the images of aggregating platelets and blot clots forming at a wound.

(Electron micrograph is from Platelets)

Nobel Laureate: Arne Tiselius

 

The Nobel Prize in Chemistry 1948.



Arne Wilhelm Kaurin Tiselius (1902-1971): "for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins"

Arne Tiselius won the Nobel Prize in 1948 for discovering how to separate protein by electrophoresis. Beginning in the early 1930's, Tiselius developed techniques for separating proteins on the basis of their migration in an electric field. Positively charged proteins move toward the cathode and negatively charged proteins move toward the anode. The trick was to detect the proteins as they move in a solution (the "moving boundary"). By the late 1930's, Tiselius had constructed a complex apparatus that detected bands of protein by recording changes in the refractive index of the solution as the boundary moved past a lens ("schlieren" method).

He used this technique to analyze the protein in blood plasma showing for the first time that the mixture was very complex and heterogeneous. The figure below is from his presentation speech. It shows that the most important proteins in human serum are albumin, various globulins (antibodies) and fibrinogen. Fibrinogen is the protein required for blood clotting.

These days electrophoresis is a common technique in biochemistry labs, especially using a gel matrix. Undergraduates easily separate complex mixtures at a resolution that Tiselius never dreamed of when he began his work 80 years ago.

The power of the technique, even with the clumsy apparatus of the 1940's was widely appreciated and that's why the Nobel Prize presenter said,

The value of the new methods which have been briefly described here, is especially brought to light by their use, which is nowadays general, in international research in biochemistry and in medicine. Tiselius' apparatuses for electrophoresis and analysis by adsorption nowadays form part of the normal equipment of a great number of laboratories and medical institutes not only in Sweden but also abroad. One notices continually in chemical periodicals new experiments made by using Tiselius' methods.

Tiselius really is the father of electrophoresis and his contribution to modern biochemistry needs to be more widely appreciated.

Religion in the United Kingdom

 
See below the fold for an explanation of the categories and more data.

Regular churchgoers:15% of UK adults go to church at least once a month. This is equivalent to 7.6 million regular churchgoers
in the UK.

Fringe churchgoers: 3% of UK adults go to church less than monthly but at least six times a year. This is equivalent to 1.6 million fringe churchgoers in the UK.

Occasional churchgoers: 7% of UK adults go to church less than six times a year but at least once a year. This is equivalent to 3.4 million occasional churchgoers in the UK.

Open de-churched: 5% of UK adults do not go to church* but they used to attend in the past and are very or fairly likely to go to church in future. This is equivalent to 2.3 million adults in the UK who are open de-churched.

Closed de-churched: 28% of UK adults do not go to church*, used to attend in the past but say they are not very or not at all likely to go to church in future. This is equivalent to 13.7 million adults in the UK who are closed de-churched.

Open non-churched: 1% of UK adults have never been to church in their life, apart from weddings, baptisms or funerals yet say they are very or fairly likely to go to church in future. This is equivalent to 0.6 million adults in the UK who are open non-churched.

Closed non-churched: 32% of UK adults have never been to church in their life, apart from weddings, baptisms or funerals and are not very or not at all likely to go to church in future. This is equivalent to 15.6 million adults in the UK who are open closed non-churched.

Other religions: 6% of UK adults, equivalent to 3.2 million people, belong to religions other than Christianity.

Unassigned: Only 162 respondents (2%) were “unassigned” because they did not answer the question on prior church attendance, although none of these had been to church in the last 12 months. A third of them attended church less than once a year or never, whilst two thirds declined to state their frequency of attendance.

* never attend or go less than once a year.

This is what a modern secular society looks like [Churchgoing in the UK]. People in Canada and the USA need to be aware of these numbers because that's where we're headed, especially in Canada. The executive summary says it all.

Two thirds of UK adults (66%) or 32.2 million people have no connection with church at present (nor with another religion). These people are evenly divided between those who have been in the past but have since left (16 million) and those who have never been in their lives (16.2 million). This secular majority presents a major challenge to churches. Most of them - 29.3 million - are unreceptive and closed to attending church; churchgoing is simply not on their agenda.

Apologists will argue that not going to church is not the same as disbelieving in God. This is true but it's a pretty good indication of how committed one is to religion.

Britain is still a country that believes in God whereas belief in a personal God has declined markedly. More than 2 in 3 (67%) of people in Britain today believe in God while 1 in 4 (26%) believe in a personal God.

In other words, 33% don't believe in God and less than half of all believers believe in a personal God. If you're a God person then the demographics does not look promising.

Making Universal Donor Type O Blood

 
An advance report that will soon be published in Nature Biotechnology describes progress toward artificially creating type O blood from A, AB, and B blood donors. The advantage is that type O blood can be given to any patient who needs a blood transfusion. If you can convert all donated blood to the universal donor then the blood supply becomes much more flexible.

The ABO blood types are determined by the presence or absence of sugar groups on proteins bound to the outer surface of red blood cells [ABO Blood Types]. A single gene is responsible for the different blood types [Human ABO Gene] and the genetics is well understood [Genetics of ABO Blood Types].

Liu et al. (2007) screened 2,500 fungus and bacterial species for enzymes that could remove the A antigens and B antigens from red blood cells.

The rationale is illustrated in this figure from their paper.

All red blood cells have H antigen. In people with type A blood the H antigen is converted to A antigen through the action of the enzyme α1,3-N- galactosaminyl transferase (GTA). GTA adds N-acetyl- galactosamine (GalNAc) to the H antigen structure. If you have blood type B then a different version of the enzyme (GTB) adds galactose (Gal) to make B antigen [see ABO Blood Types]. If neither version of the enzyme is present then H antigen will not be modified and you will have blood type O.

The authors discovered several enzymes (A-zyme) that remove GalNAc converting type A blood back to type O blood. They decided to characterize an enzyme from the flavobacterium Elizabethkingia meningoseptum that had previously been identified—and patented—in 2002. Liu et al. constucted recombinant versions of the E. meningoseptum gene and expressed it in Escherichia coli. They were able to make large quantities of active enzyme which led to crystallization and solving the structure.

A version of B-zyme was identified in the common gut bacterium Bacteroides fragilis. The gene for this enzyme was also cloned and expressed in E. coli. A modified version with high activity was selected for further study.

The two purified enzymes were used to treat blood from A, AB, and B donors. All traces of A- and B-antigens were removed as demonstrated by the lack of reactivity against anti-A and anti-B antibodies. Thus, the treated blood was effectively type O and was suitable to use as universal donor. The authors are confident that the process can be scaled up.

Accordingly, we believe that automated cost-effective processes can be developed for practical use in transfusion medicine.

Several of the authors are associated with ZymeQuest Inc. of Beverly MA (USA) and the project was funded, in part, by ZymeQuest. The authors declare their competing interest in a statement that can only be accessed from the full text version of the paper on the website. Here's the statement,

Declaration: Authors (except for G.S., J.M.N., W.S.L. and Y.V.) are employees, consultants and/or shareholders in Zymequest Inc., which holds patents covering the described technologies.

Liu, Q.P., Sulzenbacher, G., Yuan, H., Bennett, E.P., Pietz, G., Saunders, K., Spence, J., Nudelman, E., Levery, S.B., White, T., Neveu, J.M., Lane, W.S., Bourne, Y., Olsson, M.L., Henrissat, B. and Clausen, H. (2007) Bacterial glycosidases for the production of universal red blood cells. Nature Biotechnology Published online: 1 April 2007; | doi:10.1038/nbt1298.

Creationists Invade Ottawa

 
Two regulars from talk.origins have a blog called Thinking for Free. Each of them has published a report on a Creationsts meeting in Ottawa last February. Read Eamon Knight's version at Creationistist Forum -- Eamon's View and Theo Bromine's version at Creationist Forum - Theo's view.

Bio::Blogs #9

 
Bio::Blogs #9 has been posted at Public Rambling. In case you don't know, bio::blogs is a bioinformatics carnival.

Speaking of bioinformatics, it's been on my mind recently since we are just now seeing the results of our first two classes of bioinformatics undergraduates. We talked about the best way of creating an undergraduate program in bioinformatics for over ten years before we finally came up with a collaboration between the Biochemistry Department and Computer Science [Bioinformatics and Computational Biology].

The final decision was to try and educate students to be competent in both computer science and biochemistry. I was not in favor of this approach since the two disciplines are very different—that's one of the things I learned from going to computer science seminars and sitting on their graduate committees since 1992.

I think it's hard enough for students to absorb the culture of one field. To learn how researchers think in two different fields is asking too much. So far, the only students we've attracted are those who were in computer science and want to broaden their horizons by learning about bioinformatics. As I expected, they are struggling with the science courses and it's not because they are stupid. Our biochemistry students, on the other hand, are picking up a fair amount of computer training on their own without getting into information theory, database design, or theories of algorithms.

Does anyone else have experience with undergraduate programs in bioinformatics?

Mendel's Garden #13

 
 

Mendel's Garden #13 has been posted by Alex Palazzo at The Daily Transcript. Read the articles and learn about fish flakes at the same time!

Home Schooling in Missouri

 
I just don't get home schooling. How can parents think they know everything about everything? Why don't they value different points of view? I always wanted my children to be exposed to other ways of thinking and not just my way of thinking. Isn't that what education is all about?



[Hat Tip: Greg Laden]

Blood Clotting: The Basics

 
When blood vessels are damaged the leak must be sealed as rapidly as possible to prevent excess blood loss. The first response is formation of a blood clot at the site of damage. The clot is made up of cross-linked fibers made from a protein called fibrin.

The fibrin network is formed from a precursor of fibrin called fibrinogen [hear it]. Fibrinogen is a large protein that circulates freely in the blood stream. The key to understanding the mechanism of blood clot formation is in understanding how fibrinogen is converted to fibrin and why this only occurs at the site of damage to the lining of the blood vessel.

The activation mechanism is very complicated and highly regulated. The disruption of a blood clot when it is no longer needed is also complicated and highly regulated.

We'll start by looking at the basics of clot formation and dissolution.

Fibrinogen is composed of three different polypeptide chains or subunits. Each one is present in two copies (α₂β₂γ₂). The α, β, and γ chains wrap around each other to form a coiled coil triple helix. Two of these coiled coil complexes are joined head-to-head at the N-terminal ends of the polypeptides to make the complete molecule.


The complete fibrinogen molecule, which is very large as far as proteins go, consists of two domains. The central region where the N-terminal ends (N) are located forms the E domain. The outside ends where the C-terminal (C) ends are found are called the D domains.

Fibrinogen is soluble in blood plasma and the molecules show very little tendency to aggregate to form blood clots. Aggregation is prevented in large part by the N-terminal tails of the α (red) and β (blue) subunits projecting out of the central E domain. Blood clotting is initiated when these tails are chopped off by a specific protein-cutting enzyme (protease) called thrombin. Thrombin converts fibrinogen to fibrin and fibrin spontaneously aggregates to form a clot.

The activation takes place in two stages. In the first stage thrombin cleaves the α subunit releasing fibrinogen peptide A (FpA) and creating fibrin. The resulting fibrins can interact through their E domains to form filaments.

In the slower second step, the β subunit is cleaved releasing fibrinogen peptide B (FpB) and this permits aggregation of filaments to form complex networks. The resulting clot is called a soft clot. It is converted to a hard clot by Factor XIIIa (the "a" stands for "activated"). FXIIIa catalyzes the formation of covalent cross-links between fibrin molecules. The activated cross-link enzyme (FXIIIa) is formed from an inactive precursor (FXIII) by the action of thrombin. Thrombin not only cleaves fibrinogen, it also cleaves a number of clotting factors, like FXIII, to create active forms.

The initiation of clotting depends on thrombin activity. Thrombin is formed by proteolytic cleavage of inactive prothrombin to create the active protease (thrombin). This activation of prothrombin takes place at the site of injury and it's the way clotting is regulated. We'll cover it later on. You're probably getting the idea—blood clotting is controlled and regulated by a cascade of protein cleavages.

Once a clot is formed it eventually has to be dissolved once the injury is healed. This step is called fibrinolysis. The enzyme that dissolves clots is called plasmin. It chops aggregated fibrin fibers in the coiled coil region thus breaking up the clot. Can you guess how active plasmin is formed?

That's right. It's formed from a precursor called plasminogen by proteolytic cleavage. The enzyme that activates plasminogen is called tissue plasminogen activator (TPA). Plasminogen has a high affinity for fibrin clots but not for free fibrinogen. TPA also binds to fibrin and it only cleaves plasminogen when a complex of fibrin clot+plasminogen+TPA forms. The scheme on the right is a summary of what we've covered so far.

You may have heard of TPA. It's an enzyme that's given to heart attack patients but it must be delivered as soon as possible in order to prevent death. Here's what The American Heart Association says about TPA.

We strongly urge people to seek medical attention as soon as possible if they believe they're having a stroke or heart attack. The sooner tPA or other appropriate treatment is begun, the better the chances for recovery.

Tissue plasminogen activator (tPA) is a thrombolytic agent (clot-busting drug). It's approved for use in certain patients having a heart attack or stroke. The drug can dissolve blood clots, which cause most heart attacks and strokes.

Studies have shown that tPA and other clot-dissolving agents can reduce the amount of damage to the heart muscle and save lives. However, to be effective, they must be given within a few hours after symptoms begin. Administering tPA or other clot-dissolving agents is complex and is done through an intravenous (IV) line in the arm by hospital personnel.

There are very few textbooks that do a good job of summarizing and simplifying blood clotting. One of the better ones is Textbook of Biochemistry with Clinical Correlations 6th ed. edited by Thomas H. Devlin. This is an excellent book for those interested in biochemistry with a medical slant. I recommend it very highly as a reference text. It ain't cheap.

Devlin, T.H. (ed.) (2006) Textbook of Biochemistry with Clinical Correlations 6th ed., Wiley-Liss, Hoboken, N.J. (USA)

Wolberg, A.S. (2007) Thrombin generation and fibrin clot structure. Blood Reviews Jan. 5 2007. [PubMed]

Monday's Molecule #20

 
Name this molecule. The figure doesn't show the precise structure of the complete molecule but there's enough of a hint for you to figure it out. In this case we don't need a precise scientific name.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate but this one is very indirect. Nobody will be able to guess it. The bonus lunch date will be awarded to the first person to make the connection between this molecule and the University of Toronto.

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

Latest Poll on Evolution in America

 
Here's the result of the latest Newsweek Poll published on March 31, 2007. The poll was conducted by Princeton Survey Research Associates International.


These numbers don't make a lot of sense. For example, 39% of non-evangelical protestants think that God made humans only 10,000 years ago. But only 24% think that evolution is not well-supported by scientific evidence. Does that mean 15% think that evolution could be well-supported but they don't believe it anyway?

And what about the 58% of Catholics who think that evolution is supported by evidence? How did those Catholics answer the previous question? How 'bout those atheists/agnostics! Wouldn't you like to meet the 27% who think that God guided evolution or the 13% who think that humans were created quite recently? Does this mean that the "agnostics" include a significant number of believers? If so, then it suggests that calling yourself an agnostic in America is compatible with belief in the literal truth of genesis. Maybe these people have a truly sophisticated, philosophical, definition of "agnostic" in mind when they answered this question.

Public Scientific Debates

 
Sean Carrol has posted an article about pubic debates over the validity of string theory [String Theory is Losing the Public Debate]. You should read the article in order to get some idea of the "controversy." Sean thinks that string theory is in much better shape than most people realize, it's just that the supporters of string theory aren't getting their message out.

The article has attracted a number of comments including some from John Horgan and Peter Woit, both of whom are skeptical of string theory. The issue has prompted some discussion about whether public debates of scientific controversies are useful. Sean says yes,

In their rush to find evidence for the conclusion they want to reach, everyone seems to be ignoring the fact that having public debates is actually a good thing, whatever the state of health of a particular field might be. The existence of a public debate isn’t evidence that a field is in trouble; it’s evidence that there is an unresolved scientific question about which many people are interested, which is wonderful. Science writers, of all people, should understand this. It’s not our job as researchers to hide away from the rest of the world until we’re absolutely sure that we’ve figured it all out, and only then share what we’ve learned; science is a process, and it needn’t be an especially esoteric one. There’s nothing illegitimate or unsavory about allowing the hoi-polloi the occasional glimpse at how the sausage is made.

I agree, but I'd like to make an additional point. In the biological sciences there are a number of controversial issues that are not openly debated. I'm thinking of things like evo-devo, punctuated equilibria, adaptionism, RNAi, Neutral Theory, and junk DNA. What happens is that one side gets far more attention that the other so that the very existence of a controversy is buried deep in the scientific literature. Thus, it is possible to get a major grant on genomes based on the idea that Neutral Theory is wrong and there's no such thing as junk DNA. The applicant doesn't even have to justify these assumptions because the controversy isn't visible. This is wrong.

We should have more public debates on some of the topics that really are controversial in biology. (By "public" I'm usually thinking of open debates at scientific meetings.) This is becoming increasingly necessary because there are too many scientists who aren't paying attention and they don't realize that there's more than one side to a story (e.g., Animal Chauvinism, Evolution of Mammals, The Three Domain Hypothesis).

What about the downside? There is a downside and we're much more aware of it than the physics community is. We know that the public loves the debate between evolutionary biologists and Creationists because that's taken as evidence of a controversy. Evolution must not be "proven," otherwise scientists wouldn't be debating with creationists. This is a problem.

One the one hand, I think there should be much more open debate over real controversies in biology. On the other hand, I don't think we should legitimize the Creationist nonsense by debating it. I was recently invited to speak at a meeting with Michael Behe, Marcus Ross, and Paul Nelson. The topic was Intelligent Design Creationism. After some agonizing, I declined because it was apparent that these were not scientific debates in any meaningful sense of the word. How could they be when both Ross and Nelson are Young Earth Creationists? There's no scientific controversy over whether the Earth is only 10,000 years old.

So, the way I resolve this problem is to encourage public scientific debate over real science controversies but discourage public scientific debate over bogus controversies. Let's leave the non-scientific debates to the lawyers.


Via: VideoSift