Egnor Writes Me a Letter

 
read it at: A Letter To Dr. Larry Moran.

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What's Wrong with Modern Science?

 
Yesterday and today I'm hanging out with some people who care abut science education. We've had some wonderful conversations. I'm pleased to lean that there are some very smart people who think there's something seriously wrong with the way modern science is progressing. I was delighted to learn that there are a growing number of scientists who think the peer review system is broken. A lot of junk is being published.

Speaking of junk, there's an essay in this week's Nature that qualifies in more ways than one [Rise of the Digital Machine]. Mark Pagel is a biologist at Reading University (UK). He's one of those people who just can't accept the fact that humans don't have several times more genes than an insect or a nematode.
THEME

Genomes & Junk DNA

Humans are almost unimaginably complex, with trillions of cells organized into hundreds of different tissues. But we have scarcely more genes than a fruitfly or a worm, and only about four or five times as many as brewers' yeast or some bacteria. Surprising then that the human genome is 250 times larger than the yeast's. It comprises about 99% 'junk DNA' — genetic code that is not used to make the protein building blocks of life.

You know what's coming next, don't you? We're going to hear about one of the seven silly excuses for why we don't really have junk DNA (see The Deflated Ego Problem). Here's how Martin Pagel sets up his choice of excuse.

Junk DNA gives every appearance of fulfilling the metaphor of the selfish gene. It accumulates in organisms' genomes simply because it is good at accumulating; it can even be harmful. Why we put up with it has long been a mystery.

Increasingly, it seems that the genes that do code for proteins may recruit some or all of this junk DNA to regulate when, where and how much they are expressed. Because nearly every cell in the body carries a complete copy of the genome, something has to tell the genes that make eyes not to switch on in the back of the head, or genes for teeth to stay silent in our toes. Something has to instruct genes to team up to produce complex structures such as hearts and kidneys, or the chemical networks that create our metabolism and physiology.

Astute readers will see where this is going—he's going to use the "regulatory DNA" excuse. All this will accomplish is to demonstrate; (a) Martin Pagel's inability to reason like a scientist by considering evidence that has been accumulated over four decades, and (b) Nature's inability to recognize good science from bad science.

Genes, in effect, use regulation to promote their interests within the bodily phenotype: it is how they vary their exposure to the outside world. Regulation is how we can have over 98.5% similarity to chimpanzees in the sequences of our coding genes, yet differ so utterly from them.

Indeed, the huge quantity of junk DNA in the genomes of most complex organisms may act as a vast digital regulatory mechanism. Until recently many common machines, such as aeroplanes, clocks, and even computers were analogue devices, regulated by levers, springs, heat or pressure. Aeroplanes were flown with a stick, springs drove clocks. Digital regulation — instructions encoded in strings of binary numbers arbitrarily long, and hence precise — enabled complexity to increase. Stealth fighters and space shuttles are so complex that they can be flown only by digital computers, not (analogue) human pilots.

Similarly, the emergence of digital regulation derived from unused stretches of junk DNA may have precipitated the transition from single cells to complex multicellular organisms. Long runs of the four chemical bases that make up DNA can easily act like binary strings. How these stretches bind to a gene can regulate exquisitely the degree and timing of that gene's expression. Tellingly, bacteria and some other single-celled organisms have negligible amounts of junk DNA. They rely far more on analogue systems of gene regulation that are protein-based and less precise.

This is, of course, complete nonsense. We know for a fact that large amounts of the human genome are really junk. We know for a fact that you can have complex regulation by using only a small percentage of the genome (1000 bp per gene, or less than 1% of the genome, per gene is more than sufficent [Junk in Your Genome: Protein-Encoding Genes]. We know for a fact that some single-celled species (amoeba) have huge amounts of junk DNA and some some complex multicellular species have genomes that are much smaller than mammalian genomes (Drosohila melanogaster.

All these facts can be found in basic introductory textbooks. In addition, there is an abundant scientific literature on junk DNA, explaining why defective transposons (for example) really are junk. Why can't scientists like Mark Pagel, and the Nature reviewers, learn about junk DNA beore spouting off? What's wrong with science today?

Science is a process and that process involves collecting evidence and making hypotheses that explain the data. In this case the author has ignored the data showing that much of our genome is junk. He has ignored the evidence that the regulation of gene expression can be easily accomplished without invoking huge amounts of (non-conserved) DNA. He has constructed an hypothesis to explain something that doesn't need explaining; namely, why humans have the same number of genes as other mammals. He has failed to read the literature and failed to consider alternative explanations.

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Charlie Rose Science Series: The Imperative of Science

 
In case some of you didn't see the Charlie Rose show on science last week, here it is. The panelists are: Paul Nurse, Lisa Randall, Harold Varmus, Shirley Ann Jackson, and Bruce Alberts. I had a chance to congratulate both Bruce Alberts and Harold Varmus today for their excellent comments. Harold Varmus says he's been on the show several times but I don't see the show very often. Could someone please let me know the next time Charlie Rose covers a science topic?



These guys make a lot of sense. They point out that science education is a mess and that includes science education in the colleges and universities. I particularly like this comment by Harold Varmus.

I do think there's a problem in making science appear frightening and linked to a laboratory activity. As comments you've already heard suggest, science really is a process. A process by which you have ideas, you test them out, you look at evidence, you measure things, and you draw conclusions. And that's a process that applies to almost any phase of life.

Science is a process. It's a way of knowing. That's what we should be teaching.

Too many people think that science is all about doing laboratory exercises but that's actually a very poor way of teaching what science is all about. Just about anyone can be trained in the methodology of a given discipline—like biochemistry—but it takes a lot more work to teach students how to think like a scientist.

My department is currently considering a proposal to dumb down our introductory courses and reduce the numbers of lecture hours in our 3rd year courses. This would be accompanied by an expansion in the number of hours spent doing laboratory exercises. The idea is to prepare students for a career in research as though the way to become a good researcher is to learn how to pipette and not how to acquire fundamental knowledge and learn how to use it to think like a scientist.

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Molecular Biology of the Cell

 
I'm attending the 70th birthday party for Bruce Alberts in San Francisco. Here's a picture of the authors of Molecular Biology of the Cell. From left to right; Bruce Alberts, Alexander (Sandy) Johnson, Martin Raff, Keith Roberts, and Peter Walter. Julian Lewis couldn't be here.

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Pacific

 
Surf.


Surfing at Santa Cruz.



Monterey Bay.

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The Napa Valley

 
Yesterday was my very first trip to the Napa Valley. It was well worth the visit as we had a pleasant day visiting wine country. Our light lunch (above) at Domaine Chandon was a highlight.

The only bad thing about the Napa Valley is getting there (and back). It's only an hour drive from San Francisco but the roads are busy and the route is complicated—at least for tourists like us. On this occasion, however, the trip was a little more exciting because when crossing the Golden Gate bridge we encountered the protesters who were there for the Olympic torch run.

As it turns out, there were more police than protestors but the "free Tibet" and "free Burma" banners elicited a (very) few honks from passing motorists. Leslie was driving so we were one of the cars making noises. You know you're a product of the 60's when most of the protesters are the same age as you are and know how to flash a peace sign!

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Happy Birthday Genomicron

 
It's been one year since Ryan Gregory stated his blog Genomicron [One year of Genomicron. If you don't read his blog regularly, here's a chance to correct that error. Genomicron is one of the best science blogs and Ryan Gregory is one of the experts you can trust.

It's interesting to read Ryan's description of how his blog evolved from being strictly science" to one where his opinion on other things (e.g. science journalism) became increasingly important. That's a good thing, it's what bloggers bring to the table.

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Stupid Press Release

 
I was going to blog about this stupid press release from the Public Library of Science (PLoS) but RPM at evolgen beat me to it [Press Releases are Written by Stupid People].

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Does Acupuncture Work?

 
Orac is the nom-de-plume of a doctor who debunks the claims of non-evidence-based medicine (also known as "woo") on Respectful Insolence. His latest is a posting on the value of acupuncture based on recent scientific studies [Sham acupuncture is better than "true" acupuncture!]. Here's how Orac begins ...

Believe it or not, there was a time when I didn't consider acupuncture to be a form of woo.

I know, I know, it's hard to believe, given the sorts of posts I've done recently on acupuncture, but it's true. Certainly, I didn't believe the whole rigamarole about needles somehow "restoring the flow of qi" or anything like that, but I did wonder if maybe there was some physiologic mechanism at work behind acupuncture that produced real benefits in terms of pain relief above that of placebo. Sure, I may have dismissed homeopathy as the pure magical thinking that it was, but acupuncture I wasn't so sure about.

Obviously, that's changed.

The reason my opinion has changed and now I place acupuncture firmly in the "woo" category is that I've actually been reading the scientific literature on acupuncture over the last year or so....

None of us have time to investigate every form of superstition and irrational thinking. Sometimes we have to rely on trusted experts to do the required homework. Orac is one of those.

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Test Your Evolutionary Knowledge

 
Test Your Evolutionary Knowledge at Bayblab. The blog is run by a bunch of anonymous bloggers but it's pretty good anyway!

BTW, if you cheat, I will be forced to call you mean names.

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Nobel Laureate: Roderick MacKinnon

 

The Nobel Prize in Chemistry 2003.

"for structural and mechanistic studies of ion channels"

Roderick MacKinnon (1956 - ) was awarded the 2003 Nobel Prize in Chemistry for his work on the the structure and mechanism of action of the potassium (K⁺) channel. MacKinnon shared the prize with Peter Agre who discovered water channels.

The presentation speech was delivered by Professor Gunnar von Heijne of the Royal Swedish Academy of Sciences.THEME:Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

In the days of Alfred Nobel, the learned academies used to entertain and educate the public by holding open demonstrations explaining the latest scientific advances. This tradition has been largely – and perhaps unfortunately – forgotten. So let us try to revive the public demonstration of science, if only for a brief moment.

The demonstration I have in mind is a simple one, and only requires that you do something that is in any case particularly fitting for a Nobel Prize ceremony: to think. But only for exactly 5 seconds!

So, please start thinking, for 5 seconds ... Thank you!

Let us now reflect briefly on what has just happened, in each and every one of us. First, a sudden increase in the activity of the brain when you started to wonder what this is all about – should I really think at this point in the ceremony? – then, cascades of nerve signals when you were actually thinking, and finally a return to the normal resting state. And all this thinking ultimately relied on one of the simplest chemical compounds you can imagine: ordinary salt – sodium, potassium and chloride ions – streaming back and forth across the walls of your nerve cells, thereby generating the signals that activated your mind. And not even very much salt – a rough estimate is that the total amount of salt spent during these five seconds in each one of us was no more than a few grains. Only a fistful of salt to set a whole Concert Hall thinking!

And while all this brain activity was occupying our minds, our kidneys worked on quietly, as they always do, reabsorbing water from the urine to the blood. But in this case, the volumes of water transported are too big, even during five seconds, to be suitable for a demonstration from the podium.

This year's Nobel Prize in Chemistry is all about salt water, and the biochemical mechanisms that control where, when, and how often ions and water are let into or out of the cells in our body. Mechanisms that the two Laureates – Peter Agre and Roderick MacKinnon – have elucidated down to the atomic level.

Agre's was a "serendipity discovery": while working on a completely different problem, he stumbled across a protein in red blood cells that he could soon show was the water channel researchers had been looking for in vain for well over a century. His unexpected discovery opened a whole new field of study.

MacKinnon, on the other hand, decided at an early stage that he should try to do what was then thought impossible: to determine the three-dimensional structure of ion channels at atomic resolution. He bet his career on this vision – and succeeded to an extent that probably surprised even himself.

There is a lesson here, I believe: There is no one way to do science, and our support system must be sufficiently well funded and versatile to prepare the ground for both unexpected serendipity and focused, often risky, attacks on central scientific problems.

Peter Agre and Roderick MacKinnon stand for decisive contributions to the biochemistry of cell membranes, but their discoveries also have an almost tangible aesthetic component. Their work has uncovered an amazing "economy of design" in the atomic structures of the water and ion channels that is breathtaking in its simplicity and perfection. Indeed, after seeing these molecular machines, you find yourself thinking, "Of course, this is how it must be, this is how it must work!" What more could we ask of science?

Professor Agre, Professor MacKinnon, your fundamental discoveries concerning water and ion channels are singular achievements that have made it possible for us to see these exquisitely designed molecular machines in action at the atomic level. The biochemical basis for the transport of water – the most abundant and primordial substance of life – and ions – these tiny, mundane and yet absolutely essential constituents of the living world – can now be understood in unparalleled detail. On behalf of the Royal Swedish Academy of Sciences, I wish to convey to you our warmest congratulations, and I now ask you to step forward to receive the Nobel Prize in Chemistry from the hands of His Majesty the King.

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Nuclear War Is Bad for You

 
A couple of scientists at the University of Colorado have modeled what might happen if there was a nuclear war between India and Pakistan [Regional nuclear conflict would create near-global ozone hole, says CU-Boulder study].

A limited nuclear weapons exchange between Pakistan and India using their current arsenals could create a near-global ozone hole, triggering human health problems and wreaking environmental havoc for at least a decade, according to a study led by the University of Colorado at Boulder.

The computer-modeling study showed a nuclear war between the two countries involving 50 Hiroshima-sized nuclear devices on each side would cause massive urban fires and loft as much as 5 million metric tons of soot about 50 miles into the stratosphere, said CU-Boulder Research Associate Michael Mills, chief study author. The soot would absorb enough solar radiation to heat surrounding gases, setting in motion a series of chemical reactions that would break down the stratospheric ozone layer protecting Earth from harmful ultraviolet radiation, said Mills.

Wow! That sounds really bad. By the way, they forgot to mention one other nasty little detail—about 100 million people will die in the blasts and of radiation poisoning in the aftermath of the attacks.

Sort of make an ozone hole seem insignificant, doesn't it?

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The Bombardier Beetle

 
According to a report in ScienceDaily, there has been progress in understanding how the Bombardier beetle can eject such a powerful spray [The Bombardier Beetle, Power Venom, And Spray Technologies].

The bombardier beetle, found mainly in Africa and Asia, is remarkable in that it can fire a powerful jet of hot, toxic fluid to fight off predators such as birds and frogs. While the chemical reaction that makes the venom has been understood for some time, the actual power behind the venomous squirt, which can travel as far as 20cm, has been cause for speculation.

Quantities of hydroquinone and hydrogen peroxide gases build up in the beetle’s abdomen but, when necessary for defence, get mixed together in a connected ‘combustion chamber’ to produce toxic benzoquinone. This hot fluid is then fired off at force in the face of enemy predators.

Note, there isn't a problem understanding the chemical reaction and how the beetles control it. That's been well understood for several decades. You can watch a young Richard Dawkins debunking the standard creationst claims in a video posted on Genomicron [Bombardier beetles].

Ryan Gregory has followed this up with a more detailed posting that describes the evolution of bombardier beetles [Reducibly complex bombardier beetles]. Ryan was motivated to research this topic because one of the leaders of the University of Guelph creationist groups tried to use the bombardier beetle as evidence that evolution is impossible. I guess he didn't realize that this example has been refuted a long time ago.

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[Photo Credit: Institute of Physics]

Two Non-Scientists Talking about Science

 
Listen to Dr. R.C. Sproul interview Ben Stein. There are lots of very funny bits but let me pick out just one example. Here's what Ben Stein says about scientists ... (around 15 minutes)

People go into academic life in large measure because they're frightened people. They want a kind of sanctuary and uh ... so when they're attacked, or questioned even, they react very, very strongly. They're scared people, and they're really scared of Intelligent Design [Creationism] because if Intelligent Design [Creationism] is true, and if, in fact, Darwinism is ... only goes so far and only covers a small amount of the territory, all kinds of threat to their power and status arise.

Hmmmm ... I wonder why we call them IDiots?

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[Hat Tip: Evolution News & Views]

Have Your Cake and Eat It Too.

 
Matt Nisbet has tried to defend his attacks on PZ Myers and Richard Dawkins with a posting that promotes Paul Kurtz as a "reasonable" atheist [Paul Kurtz: The Local Leader Who Happens to Be an Atheist].

He followed it up with a posting on his comment policy where he notes that he has been forced to delete some of the comments from people who defend PZ Myers and Richard Dawkins [A Note On Comment Policy]. In that comment thread, Matt Nisbet defends his position on framing ...

I've been very active in communicating why my research is worth the money and I have done it very effectively.

-->I've done close to three dozen presentations over the past year and talked face-to-face with several thousand scientists, policymakers, other academics, students, and lay citizens.

-->I regularly post here on the relevance of framing to a range of topics. The top tabs of the blog explain in depth the nature and application of research to science communication.

-->I've done about 40 media interviews on issues related to science communication and/or framing.

-->I followed the Science article with an article at the WPost, a longer cover feature at The Scientist, both articles I link to as PDF copies free for reading. I have also done extended interviews on the topic at the Point of Inquiry podcast.

-->I advise and consult with a range of nonprofits, organizations, and government agencies.

-->I engage almost every serious minded blog post and comment with a respectful, and usually detailed reply.

Here's the problem. Matt Nisbet is promoting the concept of framing science. This is his field and he has every right to do that. I don't buy it and neither do many other scientists who think that framing is too close to "spin."

But that's not all that Matt Nisbet wants to do. Not only does he want scientists to adopt framing as a means to communicate science but he also wants to dictate the frame! In other words, he sets himself up as not only an expert in communication but also an expert in what should be communicated in the rationalism vs superstition debate. He can't tell the difference between the concept of framing, which many scientists reject, and his personal opinion, which is that vocal atheists are hurting the cause of atheism.

Matt want to have his cake and eat it too. He will get neither.

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[Photo Credit: Worst Birthday Cake .. Ever!]