Human Races

 
A discussion about human races has broken out in the comments to The Problem of Race .... Again. One of quesitions on that thread has come up many times in the past so I'm devoting a separate posting to the answer.

Hopefully, this will stimulate discussion and debate about the scientific data and evidence for genetically distinct humans populations. I want to get away from the other aspects of the debate about races since they always seem to devolve into accusations of racism and/or political correctness. (mea culpa)

anonymous asks,

i always feel in these discussions people are talking past each other, especially when they have differing definitions of words like 'race'. so to clarify matters for me, i would like Dr. Moran to give the likely number of races that currently exist, say something on the stability of such groupings,give examples (if possible) of these racial groupings along with their differing genetic markers e.g. race 1 - geographically located in region A & B, with unique (almost Unique) gene combination 1,3,4,5 occuring at frequencies A,B,C,E.

Are you serious? Please tell me this is a joke.

Are you one of those people who want to deny the existence of races just because your question can't be answered precisely in the manner you phrase it? That sounds very much like the kind of thinking I encounter when dealing with creationists.

Biology is messy. There are no nice and tidy boundaries around terms like race, species, or even higher taxonomic levels. You may not like it but you have to deal with it. If you understand evolution then it all makes sense and you know why things are so messy.

Our species is subdivided into many different genetically isolated(1) populations ranging from very small ones, such as the residents of Tristan da Cunha, to very large ones, such as Africans and Asians.

The term "race" usually refers to the largest populations within a species. In the case of humans, the group who migrated out of Africa founded a genetically isolated population that subsequently split into several different populations. The main ones are Asian, European, Australian, and American.

These are reasonable examples of races. Each of them can be subdivided into numerous examples of demes and populations. Their genetic distinctiveness is so obvious that most of us would have no difficulty identifying their members if we encounter them on the streets of a major cosmopolitan city.(2)

The African group from which the migrants split is "polyphyletic" and deciding how to divide it into races is problematic. However, it's clearly a group that's genetically distinct from the other races so it's not unreasonable to refer to the Africans as a race, as long as you keep in mind that there are subdivisions and that this group is much more genetically divers than the others.

The genetic distinctiveness of Africans is pretty obvious to me. I'm constantly surprised by those who pretend it doesn't exist. People of African ancestry certainly don't have any trouble recognizing that I'm Caucasian and that some of my other neighbors are Asian.

There are dozens of phylogenetic trees on the web showing these major splits and subdivisions. Probably the most famous is the mitochondrial tree but others show roughly the same tree. It would be hard to imagine anyone denying the existence of human races unless they completely reject that kind of analysis.

There are several commercial, for-profit, companies that are more than willing to take your money (and your DNA) and provide you with an analysis that identifies where your ancestors came from. They are able to do this because certain haplotypes evolved in certain parts of the world. The mitochondrial haplotypes are shown on the map above and the Y-chromosome haplotypes are shown on the map on the left.

Given all the publicity about tracing your genealogy by haplotyes and all the scientific papers on the genetic differences between races, it surprises me that in 2009 there are still people who question whether these genetic differences even exist.

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1. "Genetically isolated" does not mean that there's no genes flow between populations. It means restricted gene flow. If gene flow was zero they the populations wouldn't be populations. They would be species.

2. This does not mean that there won't be examples where the identification is difficult and it doesn't deny the existence of interbreeding between races. If you're looking for that kind of example then you won't find it in humans or in any other species where the biological term race is commonly used.

[Photo Credit: Downtown Toronto]

Shame on Norway!

 
The 2009 Nobel Peace Prize was announced today by Thorbjørn Jagland, Chairman of the Norwegian Nobel Committee. It goes to President Barack Obama, a man who has been President of the United States for about nine months and is currently conducting two simultaneous invasions and occupations of foreign nations.

The United States "peaceably" threatens both Iran and North Korea with possible military strikes if they do not stop developing a nuclear weapons program. The United States deploys the largest, most deadly, military force the world has ever seen and is in no hurry to reduce its size.

I think Obama is a wonderful choice for President of the USA. He is far, far, better than many others who have sought that office. However, it does not follow from that that he merits the Nobel Peace prize. He doesn't. The Norwegian Nobel Committee should be ashamed of themselves.

Here's the press release. The committee is confusing hope and hype with actual results. Let's hope the promise of a better world works out over the course of the next few years or we might look back on this award with shock and awe. At the very least, we should expect a serious reduction in the American nuclear weapons stockpile, right? And we should expect UN Nuclear inspection teams to be visiting the USA, Russia, France, Great Britain, China, India, Pakistan, and Israel.

Who's holding their breath?

The Nobel Peace Prize for 2009

The Norwegian Nobel Committee has decided that the Nobel Peace Prize for 2009 is to be awarded to President Barack Obama for his extraordinary efforts to strengthen international diplomacy and cooperation between peoples. The Committee has attached special importance to Obama's vision of and work for a world without nuclear weapons.

Obama has as President created a new climate in international politics. Multilateral diplomacy has regained a central position, with emphasis on the role that the United Nations and other international institutions can play. Dialogue and negotiations are preferred as instruments for resolving even the most difficult international conflicts. The vision of a world free from nuclear arms has powerfully stimulated disarmament and arms control negotiations. Thanks to Obama's initiative, the USA is now playing a more constructive role in meeting the great climatic challenges the world is confronting. Democracy and human rights are to be strengthened.

Only very rarely has a person to the same extent as Obama captured the world's attention and given its people hope for a better future. His diplomacy is founded in the concept that those who are to lead the world must do so on the basis of values and attitudes that are shared by the majority of the world's population.

For 108 years, the Norwegian Nobel Committee has sought to stimulate precisely that international policy and those attitudes for which Obama is now the world's leading spokesman. The Committee endorses Obama's appeal that "Now is the time for all of us to take our share of responsibility for a global response to global challenges.

What does the White House have to say? Surprisingly, Obama is being very candid.

"I am both surprised and deeply humbled," Obama said at the White House.

"I do not view it as a recognition of my own accomplishments. But rather as an affirmation of American leadership. ... I will accept this award as a call to action."

Obama said he did not feel he deserves "to be in the company" of past winners, but would continue to push a broad range of international objectives, including nuclear non-proliferation, a reversal of the global economic downturn, and a resolution of the Arab-Israeli conflict.

He acknowledged the ongoing U.S. conflicts in Iraq and Afghanistan, noting that he is the "commander in chief of a country that is responsible for ending" one war and confronting a dangerous adversary in another.

The Associated Press story seems to be typical of the responses from around the world [President Barack Obama wins Nobel Peace Prize]. I think this is going to make Obama's life more difficult, not easier. It may have the exact opposite effect to what well-meaning members of the prize committee expected. This will go down as one of the most controversial awards in recent memory.

Many observers were shocked by the unexpected choice so early in the Obama presidency, which began less than two weeks before the Feb. 1 nomination deadline and has yet to yield concrete achievements in peacemaking.

Some around the world objected to the choice of Obama, who still oversees wars in Iraq and Afghanistan and has launched deadly counter-terror strikes in Pakistan and Somalia.

Members of the Norwegian Nobel Committee said their choice could be seen as an early vote of confidence in Obama intended to build global support for his policies. They lauded the change in global mood wrought by Obama's calls for peace and cooperation, and praised his pledges to reduce the world stock of nuclear arms, ease American conflicts with Muslim nations and strengthen the U.S. role in combating climate change.

Aagot Valle, a lawmaker for the Socialist Left party who joined the committee this year, said she hoped the selection would be viewed as "support and a commitment for Obama."

"And I hope it will be an inspiration for all those that work with nuclear disarmament and disarmament," she told The Associated Press in a rare interview. Members of the Nobel peace committee usually speak only through its chairman.

The peace prize was created partly to encourage ongoing peace efforts but Obama's efforts are at far earlier stages than past winners'. The Nobel committee acknowledged that they may not bear fruit at all.

"He got the prize because he has been able to change the international climate," Nobel Committee chairman Thorbjoern Jagland said. "Some people say, and I understand it, isn't it premature? Too early? Well, I'd say then that it could be too late to respond three years from now. It is now that we have the opportunity to respond — all of us."

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The Food Industry Depends on the Fact that Evolution Doesn't Happen!

 
Nobody has ever seen life created in peanut butter.

This is one of those videos where you don't know whether to laugh, or cry.

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[Hat Tip: John Pieret at Thoughts in a Haystack: Peanut Butter and Bananas ... Yum!]

I'm Starting an Evolution Revolution

 
The University of Toronto is in the process of reorganizing its introductory biology courses. The new proposal is to offer two half courses in first year and two in second year. The expectation is that all life science students will take all four courses.

To give you an idea of the numbers, the anticipated enrolment for the first year courses is 1920 students and for the second year courses about 1500 students. These are the courses that will make the biggest impact on our students when it comes to understanding basic biology.

Here they are ....

BIO120H: Adaptation and Biodiversity
BIO130H: Molecular and Cell Biology

BIO220H: From Genomes to Ecosystems in a Changing World
BIO230H: From Genes to Organisms

There's a lot that's wrong with this proposal but I'm focusing on the teaching of evolution. Everyone agrees that it's important to teach evolution and teach it correctly. I don't think a course entitled "Adaptation and Biodiversity" is going to do an adequate job, especially since the fossil record is completely ignored and there's no serious attempt to teach the history of life. Population genetics gets only a single lecture in the middle of the course.

I'm trying to start a revolution by convincing my colleagues to vote down these proposals on the grounds that we can do much better. At the very least, the decision should be postponed for a year so we can debate the issues. The proposals were first circulated last week and the recommendation of the Life Sciences Curriculum Committee is going to be decided today. If they recommend in favor of adopting the proposals, then it's highly unlikely that the recommendation will be overturned at the next level. That's no way to run a university.

Yesterday I bumped into my colleague, Paul Hamel, as I was on my way to Tim Hortons. He asked me what I was up to and I told him I was trying to start a revolution. His advice? "Don't quit your day job!"

(In order to appreciate this comment, you probably need to know that Paul is one of the most radical members of our faculty and he's been fighting to change the system, and our society, for several decades.)

I think most of you can see the problem with the BIO120H course title. The first sentence of the course description is, "Principles and concepts of evolution and ecology related to origins of adaptation and biodiversity." Since much of the biodiversity around us is not due to adaptation, it seems like a strange way to describe "principles and concepts."

That's not the only thing wrong with the courses but this isn't the place to go into more detail. The problem I face is that it is very difficult to convince my colleages that there's something wrong with the way we propose to teach evolution since very few of them understand evolution. In my case the problem is compounded by the fact that the course instructor, Spencer Barrett, is a highly respected evolutionary biologist with lots of publications in prestigious journals.

I'm not optimistic. Making changes at a big university is like trying to herd together a bunch of cats and get them to cooperate in turning a full loaded supertanker. It can be done but it's a lot of work.

Anyway, this is a long-winded introduction to the real reason for this posting. I want to highlight a posting by Ryan Gregory who explains why it's important to teach evolution and what level of detail is needed [How detailed an understanding of evolution do we need?]. Here's a teaser, get on over to Genomicron and read the whole thing.

If you mean “students enrolled in science programs,” either undergraduates or grad students (as in our study), then I would say that a good working knowledge of evolutionary theory, though not a full understanding of all its nuances, should be a major goal. Again, evolution is the unifying principle of biology, and without grasping how it works, one cannot make sense of the history and current diversity of life on this planet.

UPDATE: The committee met and the courses were approved without much debate.

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Columbine and Creationism: A Case Study

 
Here's an excellent example of the fallacious argument referred to as "guilt by association." The idea is that you develop an association between some evil person and the position you want to attack.

For example, suppose you wanted to show that fundamentalist Christianity was bad. What you do is find some fundamentalist Christian who behaved immorally—not hard to do—then allow readers to draw the "obvious" conclusion.

Or, you could do the same thing with those who accept evolution as Barry Arrington does on Uncommon Descent [Darwin at Columbine Redux].

As the attorney for the families of six of the students killed at Columbine, I read through every single page of Eric Harris’ jounals; I listened to all of the audio tapes and watched the videotapes, including the infamous “basement tapes.” There cannot be the slightest doubt that Harris was a worshiper of Darwin and saw himself as acting on Darwinian principles. For example, he wrote: “YOU KNOW WHAT I LOVE??? Natural SELECTION! It’s the best thing that ever happened to the Earth. Getting rid of all the stupid and weak organisms . . . but it’s all natural! YES!”

Elsewhere he wrote: “NATURAL SELECTION. Kill the retards.” I could multiply examples, but you get the picture.

It was no coincidence that on the day of the shootings Harris wore a shirt with two words written on it: “Natural Selection.”

I am not suggesting that Auvinen’s and Harris’ actions are the inevitable consequences of believing in Darwinism. It is, however, clear that at least some of Darwin’s followers understand “survival of the fittest” and the attendant amorality at the bottom of Darwinism as a license to kill those whom they consider “inferior.” Nothing could be more obvious.

For the record, I reject all attempts to discredit Christianity by pointing to priests who molest children; the fact the Kent Hovind is in prison; or the tribulations of Jimmy Swaggart. We can gloat about those incidents and revel in the hypocrisy but they say nothing at all about the truth of Christianity.

Similarly, I do not apologize for nor condone the behavior of stupid people who accept evolution. It's irrelevant to the debate over the facts of evolution.

Everyone should adopt this position. Unfortunately, there are quite a few people on the other side who get all uppity whenever a Christian is caught with his pants down but see nothing wrong with blogging about evil evolutionists.

The word you're looking for is "hypocrisy." It seems to be quite common on that side of the debate.

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Junk DNA: A Case Study in Scientific Controversy

 
I strongly support the concept of junk DNA and I reject the idea that a significant percentage more than 10% of the DNA in our genome has a function. This is my informed opinion.

This is a genuine scientific controversy, one that I bring to the attention of my students. We are discussing controversies, misunderstandings, and frauds. This one counts as a scientific controversy.

Of course, it's also part of the rationalism vs superstition debate since creationists have a hard time explaining junk DNA. The Intelligent Design Creationists, in particular, are almost duty-bound to oppose the concept. For an excellent example of how the IDiots exploit a genuine scientific controversy see: How The Junk DNA Hypothesis Has Changed Since 1980 by Richard Sternberg .

THEME

Genomes & Junk DNA
It all sounds very much like science. The trick is to put as much science into the discussion as possible, while keeping the distortions and misrepresentations to a mimimum. It's best to omit all references to other points of view 'cause that gives the impression that the scientific community is opposed to junk DNA.

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One Nation Under God

 

Here's a little quiz. What nation is being referred to here?

Right. Boy, you guys are clever.

This image is so disgusting on so many levels that one hardly knows where to begin. Fortunately, I suspect most of you have already seen the PZ Myers take-down of a few days ago [The goggles! They do nothing!].

I couldn't resist re-posting the image. If you visit the websit at McNaughton Fine Art you'll get an added bonus. You can mouse over any of the figures and get an explanation.

Look in the lower-right corner. Why is that Supreme Court Justice holding his head in his hands?

Who is that person with his arm partially raised at the bottom of the picture in the lower-left corner? Why that's an immigrant, don't you know?

Why does he have his hand up like that? There are many good people in America, they are not all Christian. I wanted him to have a look of shock when he realizes where the source of America's greatness comes from as he sees Christ holding the Constitution. We live in a country where we are free to worship as we please.

My favorite is the Professor, sitting on the top step in the lower-right.

He tightly hold his "Origin of Speces" book by Charles Darwin. This represents the liberal lefts control of our educational system. His smug expression describes the attitude of many of the educational elite. There is no room for God in education. There is contempt for any other viewpoints. Humanism dominates the educational system of America and I believe that is wrong. Notice that he is the only one sitting on the top step. He tries to place himself on an equal footing with God, but he is still nothing next to the intelligence of the Creator.

For even more fun and games, try and guess which Presidents get to walk with Jesus and which ones are left out?

Who is your favorite person? Can you find Satan? How about Waldo? (Wally?)

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Boring ....

 
Chris Mooney, Matt Nisbet, and Josh Rosenau got their knickers in a knot last week for thinking the Richard Dawkins had become an accommodationist [see Is Richard Dawkins an Accomodationist?].

Dawkins promptly denied it. That leaves these three accommodationists will little choice but to apologize for being so stupid. For an example of how Chris Mooney admits he was wrong (not) see his latest posting: How Richard Dawkins Communicates Evolution (Surprise, It's Not the Same Thing as Atheism).

PZ Myers takes the time to demolish the Mooney posting using images of sad puppies [My regrets on your traumatic brain damage!]. It ain't pretty.

My concern is that Chris Mooney isn't holding up his end of the fight. His postings are becoming quite boring.

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The Problem of Race .... Again

 
The current politically correct view of human races is that they don't exist. Surprisingly, this view has been adopted by many scientists, including biologists, who should know better.

Bruce T. Lahn and Lanny Ebenstein have published an opinion piece in this week's issue of Nature. Everyone should read it [Let's celebrate human genetic diversity].

They begin by pointing out the problem and then they state their position.

The current moral position is a sort of 'biological egalitarianism'. This dominant position emerged in recent decades largely to correct grave historical injustices, including genocide, that were committed with the support of pseudoscientific understandings of group diversity. The racial-hygiene theory promoted by German geneticists Fritz Lenz, Eugene Fischer and others during the Nazi era is one notorious example of such pseudoscience. Biological egalitarianism is the view that no or almost no meaningful genetically based biological differences exist among human groups, with the exception of a few superficial traits such as skin colour3. Proponents of this view seem to hope that, by promoting biological sameness, discrimination against groups or individuals will become groundless.

We believe that this position, although well-intentioned, is illogical and even dangerous, as it implies that if significant group diversity were established, discrimination might thereby be justified. We reject this position. Equality of opportunity and respect for human dignity should be humankind's common aspirations, notwithstanding human differences no matter how big or small. We also think that biological egalitarianism may not remain viable in light of the growing body of empirical data (see box).

These guys seem to be a bit late in realizing that the scientific data doesn't support the politically correct "biological egalitarianism" viewpoint but, as they say, better late than never.

Here's their bottom line.

• Promoting biological sameness in humans is illogical, even dangerous
• To ignore the possibility of group diversity is to do poor science and poor medicine
• A robust moral position is one that embraces this diversity as among humanity's great assets

Bravo! I'm glad that more and more scientists are speaking out on this issue.

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Lahn, B.T. and Ebenstein, L. (2009) Let's celebrate human genetic diversity. Nature 461:726-728 [Nature]

[Hat Tip: Nils Reinton at BIOpinionated: I Wish I Wrote This (me too! -LAM)]

Tomorrow's Weather: 40% Chance of Rain

 
When you are told that there's a 40% chance of rain tomorrow, what do you think? When you see the hourly forecasts and learn that for each hour in the morning there's a 40% chance of rain but in the afternoon there's only a 30% chance of rain in each hour, what do you think?

Find out how to interpret these numbers by reading Nick Anthis at The Scientific Activist: Bad Math at The Weather Channel.

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[Photo Credit: South African National Parks]

The Ribosome and the Central Dogma of Molecular Biology

The Nobel Prize website usually does an excellent job of explaining the science behind the prizes. The STRUCTURE AND FUNCTION OF THE RIBOSOME is a good explanation of reasons why the 2009 Nobel Prize in Chemistry was awarded for work on the ribosome.

Unfortunately, the article begins by perpetuating a basic misunderstanding of the Central Dogma of Molecular Biology.

The ribosome and the central dogma. The genetic information in living systems is stored in the genome sequences of their DNA (deoxyribonucleic acid). A large part of these sequences encode proteins which carry out most of the functional tasks in all extant organisms. The DNA information is made available by transcription of the genes to mRNAs (messenger ribonucleic acids) that subsequently are translated into the various amino acid sequences of all the proteins of an organism. This is the central dogma (Crick, 1970) of molecular biology in its simplest form (Figure 1)

This is not the Central Dogma according to Crick (1970). I explain this in a posting from two years ago [Basic Concepts: The Central Dogma of Molecular Biology].

In both his original paper (Crick, 1958) and the 1970 update, Crick made it very clear that the Central Dogma of Molecular Biology is ....

The Central Dogma. This states that once “information” has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.

The diagram that's usually attributed to the central dogma is actually the Sequence Hypothesis. Crick was well aware of the confusion and that's why he wrote the 1970 paper. It was at a time when the so-called "Central Dogma" had been "overthrown" byt the discovery of reverse transcriptase.

Since then the false version of the Central Dogma has been disproven dozens and dozens of times—it's a minor cottage industry.

Here's what Crick says about this false version of the Central Dogma in his 1970 paper—the one quoted at the top of this page.

It is not the same, as is commonly assumed, as the sequence hypothesis, which was clearly distinguished from it in the same article (Crick, 1958). In particular, the sequence hypothesis was a positive statement, saying that the (overall) transfer nucleic acid → protein did exist, whereas the central dogma was a negative statement saying that transfers from protein did not exist.

Let's try and get it right. It will have the great benefit of stopping us from putting up with any new papers that refute the Central Dogma of Molecular Biology!

It will also encourage critical thinking. Haven't you ever wondered why there is a Central Dogma when reverse transcriptase, splicing, epigenetics, post-translational modification, chromatin rearrangements, small regulatory RNAs, and just about everything else under the sun, supposedly refutes it?

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Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163,

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

2009 Nobel Prize in Chemistry

 
"for studies of the structure and function of the ribosome"

This one's not unexpected. Almost everyone knows that there should be a Nobel Prize for the ribosome [see Nobel Prize Predictions]. Problem is, Harry Noller was on most people's short list. He's been working on the problem since 1968 and has published more than 200 papers on ribosome structure and function. This is going to be a controversial decision.

Here's the press release.

Press Release

7 October 2009

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2009 jointly to

Venkatraman Ramakrishnan, MRC Laboratory of Molecular Biology, Cambridge,
United Kingdom

Thomas A. Steitz, Yale University, New Haven, CT, USA

Ada E. Yonath, Weizmann Institute of Science, Rehovot, Israel


"for studies of the structure and function of the ribosome"


The ribosome translates the DNA code into life

The Nobel Prize in Chemistry for 2009 awards studies of one of life's core processes: the ribosome's translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year's Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

An understanding of the ribosome's innermost workings is important for a scientific understanding of life. This knowledge can be put to a practical and immediate use; many of today's antibiotics cure various diseases by blocking the function of bacterial ribosomes. Without functional ribosomes, bacteria cannot survive. This is why ribosomes are such an important target for new antibiotics.

This year's three Laureates have all generated 3D models that show how different antibiotics bind to the ribosome. These models are now used by scientists in order to develop new antibiotics, directly assisting the saving of lives and decreasing humanity's suffering.

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Another View of Science

I received this email message from Arv Edgeworth. It represents a serious point of view held by a large number of people. He gave me permission to post it. I'll respond in the comments.

I'm not a scientist, nor a professor of science, nor a son of a scientist, but I do love science.  I have collected over 150 science textbooks, that run from 1934 to 2006.  I'm responding to your article: "Do Graduate Students Understand Evolution?"  My greatest concern isn't that students views of evolution are flawed.  My greatest concern is not just with the students, but with professors as well, not understanding the limits of science.  I'm concerned that most professors at universities could not tell you where their science ends, and their philosophical worldview begins.  I believe modern science has a blindspot.  Sad to say, real science isn't what it used to be.

As the old science joke says: "Tell me who is funding the research, and I'll tell you the result."  I believe there are certain assumptions that the majority of scientists start out with today, based on their philosophical worldview, not the scientific evidence.  They interpret all the evidence in light of their worldview, then use their interpretation of the evidence as proof that their worldview is correct. Starting with different assumptions will always result in different conclusions.  My concern is that the majority of students, scientists, and professors of science cannot separate what they know from what they just believe, and I doubt if they would recognize the difference.

The amount of speculation and opinion that is being passed off as fact today in the name of science boggles the mind.  Scientific inquiry is being stiffled as students are not truly being trained how to think, they are just being told what to think.  Students many times are being indoctrinated, not educated.

I'm sure you are enamored with evolution theory, but why are trillions of dollars in funding and research being spent on trying to prove this theory is true, and we still don't have a cure for cancer?  Or do we?  I guess that could be debated.  After all, there is a lot of money in it.  How many scientists just spent 17 years trying to put Ardi's bones together from fossilized pieces of bone that were squished to smithereens and so badly decayed that a single touch turned the bones to dust?  One group of scientists gave conclusions of ape characteristics and one group gave conclusions of human characteristics.  Must be a "missing link."  I'm sure you probably dislike that term.  Could each group have had presuppositions?  I'm sorry but I have a hard time justifying this nonsense, and for what?  I had a dog that spent its whole life digging in the ground for bones too, but I never thought the government should pay his salary.

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Monday's Molecule #139

 
The molecule is 4-sulfonamide-2',4'-diaminobenzol or "Prontosil," a potent antibiotic. Gerhard Domagk received the Nobel Prize for developing Prontosil as a treatment against bacterial infections.

The overall winner is Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany. The undergraduate winner is Jason Oakley a biochemistry student at the University of Toronto.

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Name this molecule. The common name will do. Briefly describe what it does.

There's a Nobel Prize directly connected to this molecule. If you can name the molecule then you can find the Nobel Laureate(s).

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only four ineligible candidates for this week's reward: Philip Johnson of the University of Toronto, Ben Morgan of the University of North Carolina at Chapel Hill, Frank Schmidt of the University of Missouri and Joshua Johnson of Victoria University in Australia.

Frank and Joshua have agreed to donate their free lunch to an undergraduate. Consequently, I have an extra free lunch for a deserving undergraduate so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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IDiots and Telomeres

 
Today's Nobel Prize announcement has prompted the usual stupidity from the creationist crowd. They don't get things right very often but when they rush into print their track record is even worse. You'd think they would have learned by now.

Most, but not all, bacteria have circular chromosomes. This is undoubtedly the primitive condition of living cells—at least once life got underway.

The advantage of a circular chromosome is that it doesn't have any free ends. This is important for two reasons: (1) nucleases that chew up nucleic acids like to work on free ends so having a circular chromosome increases the stability of the chromosome, and (2) circular chromosomes avoid the problems with replicating the ends of DNA.

That last reason needs a little explanation. DNA replication is complicated because evolution has only produced one kind of polymerase enzyme—the kind that works exclusively in the 5′→3′ direction.¹ This creates a problem when replicating double-stranded DNA because the strands run in opposite directions.

The DNA replication complex (replisome) has evolved a solution to this problem as illustrated in the diagram. As replication proceeds from right to left, one of the strands is copied directly by a DNA polymerase molecule. This new strand is called the leading strand. The other strand is copied by a separate DNA polymerase molecule but it has to run backwards. That strand, the lagging strand, is made in short pieces that have to be stitched together. Every now and then a new lagging strand fragment (Okazaki fragment) is initiated using a special RNA primer.

This is not a very good design but it's the only thing that could evolve given that polymerases can only go in one direction. Most of us could have easily designed an better way of replicating DNA if we were in charge. While we were at it we could have designed nucleases that don't attack genes.

The DNA replication complex may be messy but it works. At least it works with circular DNA. When you have free ends there's a bit of a problem. Look at the diagram. You can see that when the replication fork reaches the end on the left, the leading strand will be complete. However, there will likely be a gap at the very end where the lagging strand didn't initiate a new Okazaki fragment. When the replisome dissociates this gap will persist.

As strands continue to be replicated over and over there will be a progressive shortening of the chromosome because of the inefficiency of the replication process.

There are several ways of handling this problem. Some bacteriophage with linear chromosomes form circles during replication in order to avoid shortening. In bacteria, there are two different mechanisms for dealing with the problem. Either the ends of the two strand are covalently joined, creating a hairpin, or a protein is covalently attached to the end of one strand [see Bacterial Chromosomes]. Either way is effective in preventing chromosome shortening during replication.

Eukaryotes have evolved a third mechanism. The ends of eukaryotic chromosomes have extensive repeat segments called telomeres. This works because the repeats can be shortened for many generations before the "business part" of the chromosome is affected. The repeats can also be extended from time to time by telomerase. This restores the parts that are lost during replication. The copying is crude, but effective. It uses an RNA template that's part of the telomerase.

The net effect is that telomeres protect the ends of eukaryotic chromosomes. This protection is due to the fact that cells have nucleases that can chew up DNA and because the DNA replication machinery has a built-in flaw that doesn't allow it to copy the very ends of double-stranded DNA. All in all you'd have to say that if this was designed then it must have been Rube Goldberg who built it!

This year's Nobel Prize in Physiology & Medicine was awarded to Elizabeth Blackburn, Carol Greider and Jack Szostak for their work on telomeres and telomerase.

Within hours, DLH posted an article n Uncommon Descent [DNA Preservation discovery wins Nobel prize].

Were one to design the encoded DNA “blueprint” of life, would not one incorporate ways to preserve that “blueprint”? The Nobel prize in medicine has just been awarded for discovery of features that look amazingly like design to preserve chromosomes ....

These telomeres can probably be shown to be essential to survival, and are likely to be irreducibly complex. If so, how can macro evolution explain the origin of this marvelous preservation feature that appears to be an Intelligent Design?

Chromosome ends need "protection" because the designer couldn't figure out how to have safe nucleases in a cell and couldn't figure out how to replicate the ends of double-stranded DNA molecules. Several different mechanisms have evolved for dealing with these problems. Telomeres are one solution.

The telomeric repeats evolved from internal repeat sequences. Telomerase is a reverse transcriptase and it likely evolved from a retrovirus-encoded reverse transcriptase. In Drosophila there are no telomers and there isn't a telomerase, Instead, the chromosome ends are protected by multiple copies of defective transposons.

The IDiots are going to have to look elsewhere for evidence of God.

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1. There are good reasons for this. They have to do with the acccuracy of DNA replication and proofreading, but that's a story for another posting.