The Place of Science in Federal Government

I am subscribed to Seed Magazine, and I read the interview with Bush's point man on science, National Science Advisor John Marburger, the other day with little surprise as he tried to boast of his president's accomplishments:

Seed: What do you regard as your greatest accomplishment?

JM: In a job like this, the most important accomplishment is to make sure that this vast machinery of science continues to move forward and produce the kind of results that have made America strong and great and an exciting place to be a scientist. And I believe that history will show that under this administration, science and technology have thrived as well as they could, given the constraints that we work under. Those constraints are very great. Not least of which is having a very unpopular president, very difficult foreign policy, wars, and unpopular policies of various kinds. Those notwithstanding, I'm satisfied that I've done everything that I could to make science work for the nation. I think that future presidents will find it difficult to compile a record as long as this one. In retrospect, it will be seen that this was a tough act to follow.

He went on in this vein, talking about how much of US GDP Bush invested and how that would be a "tough act to follow." The problem is this little thing called fact. From the NRC report in 2007*, quote, "In 2001 (the most recent year for which data are available), U.S. industry spent more on tort litigation than on research and development. Federal funding of research in the physical sciences, as a percentage of Gross Domestic Product, was 45 percent less in FY 2004 than in FY 1976." Tough act to follow?

In part because of Republicans' views on trade and laissez-faire capitalism, science jobs and technology jobs are being exported like never before. From the same report, "The United States is today a net importer of high-technology products. Its trade balance in high-technology manufactured goods shifted from plus $54 billion in 1990 to negative $50 billion in 2001."

Also, the tendency for US students to go into science and technology fields is getting worse and worse, "In South Korea, 38 percent of all undergraduates receive their degrees in natural science or engineering. In France, the figure is 47 percent, in China, 50 percent, and in Singapore, 67 percent. In the United States, the corresponding figure is 15 percent."

I think that the Obama administration faces budget challenges (Bush squandered a surplus and left Obama a $1 TRILLION deficit his first year), but sees things exactly the way the NAS report does:

"Without a renewed effort to bolster the foundations of our competitiveness, we can expect to lose our privileged position. For the first time in generations, the nation’s children could face poorer prospects than their parents and grandparents did. We owe our current prosperity, security, and good health to the investments of past generations, and we are obliged to renew those commitments in education, research, and innovation policies to ensure that the American people continue to benefit from the remarkable opportunities provided by the rapid development of the global economy and its not inconsiderable underpinning in science and technology."

We'll wait and see. In the meanwhile, picking Holdren to replace Marburger was a very, very good decision.

One of the tough decisions that our president will have to make is shifting the billions and billions of dollars spent on weapons-technology programs and weapons R&D to creating jobs dealing with improving green technology and combatting climate change. People will say he's "soft" until they realize that our greatest threat is not China challenging us on a battlefield but the gaping hole in our economy that has partly resulted from our energy and technology policies, as well as fair versus free trade agreements.

* National Research Council, 2007, Rising Above the Gathering Storm: Energizing and Employing America for a Brighter Economic Future, The National Academies Press, Washington, D.C.

The anthropic principle revisited

This month's issue of Seed alerted me to something that I have mentioned before and think may just destroy the factual basis of the fine-tuning argument for a God's existence. Imagine that instead of arguing that the physical constants are fine-tuned so that they cannot be independently varied, we actually did a mathematical analysis of them to see how the ratios of the constants could be changed but still produce life. In a peer-reviewed article entitled, "Limitations of anthropic predictions for the cosmological constant Λ: cosmic heat death of anthropic observers", Fred C. Adams at Michigan looked at the relationships of gravity and the nuclear forces as fundamental physical constants and found that so long as these are varied together, they produce a number of star-sustaining, and therefore life-sustaining, physical universes.

In this latter case, the bounds on a Λ [the cosmological constant] can be millions of times larger than previous estimates—and the observed value. We thus conclude that anthropic reasoning has limited predictive power.

Theists often use the anthropic principle to argue in favor of an intelligent designer of the universe. Given that the idea of the argument precludes the designer being a part of the universe, this is all but arguing for the existence of God, not just some alien somewhere. The argument usually goes, "If you changed the force of gravity by even one-quadrillionth of a N, then life couldn't exist..."

You can view this sort of argument here and here by Collins. A substantive reply to Collins' argument follows:

Collins is more persuasive, although certainly not original, when trotting out the Anthropic Principle, the argument that the universe is uniquely pre-tuned to bring about life in general and human life in particular. There are a number of physical constants and laws such that if any had been even slightly different, life might well have been impossible. For example, for roughly every billion quarks and antiquarks, there is an excess of one quark – otherwise, no matter. If the rate of expansion immediately after the Big Bang had been a teeny tiny fraction smaller than it was, the universe would have recollapsed long ago. If the strong nuclear forces holding atomic nuclei together had been just a smidgeon weaker, then only hydrogen would exist; if a hair stronger, all hydrogen would promptly have become helium, and the solar furnaces inside stars –which we can thank for the heavier elements – would never have existed.

Both Dawkins and Sagan also examine this argument, which Dawkins caricatures as "god-as-dial-twiddler." It is oddly tautological, in that if the universe were not as it is, we indeed would not be here to wonder about it. In Fred Hoyle's science fiction novel, The Black Cloud, it is explained that the probability of a golf ball landing on any particular spot is exceedingly low – and yet, it has to land somewhere! The Anthropic Principle can also be "solved" by multiple universes, of which ours could simply be the one in which we exist; this might apply not only to horizontally existing multi-verses, but to the same one occurring differently in time if there have been (and will be) unending expansions and contractions. Moreover, it isn't at all clear that the various physical dials are independent, or that the physical constants in the universe could be any different, given the nature of matter and energy.

This is a typical response to the theistic position --

1) pointing out that improbable events happen all the time without being of divine origin: each seven-card hand dealt in stud poker has a probability of (1/52*1/51*1/50*1/49*1/48*1/47*1/46) = 1 in 674,274,182,400. But does that make it a miracle?
2) questioning whether the constants can be changed at all, or if they are primally fixed by the nature of the universe
3) invoking the multiverse to reduce the significance of any one universe's "uniqueness" in a statistical sense (also see here)

But from a scientist's standpoint, it's much more interesting to wonder what ratios and relationships amongst the physical constants would still produce life if they were varied interdependently. And that's the question that has been answered by Fred Adams. There are many configurations of the constants that, when varied together, still produce life-friendly, or "Goldilocks"-zone universes. This makes the anthropic principle much less interesting. Yet another reason to give up on the idea of a God.

Pretty random thing

A student that I had last year, who I genuinely like, came by randomly Friday and asked me, "What do evolutionists think happens after we die?"

After I corrected his notion that all believers in sound biology are necessarily non-believers in an afterlife, I used the frequent parallel between "before you were born" and "after you die" to try to explain what it means to lose consciousness.

By coincidence, Sunday, I read this article in SciAm: "Never Say Die - Why We Can't Imagine Death".

Today, I saw this and giggled.

Politics notes

Following up an earlier item about the growing gulf between the GOP's policies and science's reality, the 63rd Nobel Prize winner has now endorsed Obama. The text of the letter which the signatories affirm:

This year's presidential election is among the most significant in our nation's history. The country urgently needs a visionary leader who can ensure the future of our traditional strengths in science and technology and who can harness those strengths to address many of our greatest problems: energy, disease, climate change, security, and economic competitiveness.

We are convinced that Senator Barack Obama is such a leader, and we urge you to join us in supporting him.

During the administration of George W. Bush, vital parts of our country's scientific enterprise have been damaged by stagnant or declining federal support. The government's scientific advisory process has been distorted by political considerations. As a result, our once dominant position in the scientific world has been shaken and our prosperity has been placed at risk. We have lost time critical for the development of new ways to provide energy, treat disease, reverse climate change, strengthen our security, and improve our economy.

We have watched Senator Obama's approach to these issues with admiration. We especially applaud his emphasis during the campaign on the power of science and technology to enhance our nation's competitiveness. In particular, we support the measures he plans to take – through new initiatives in education and training, expanded research funding, an unbiased process for obtaining scientific advice, and an appropriate balance of basic and applied research – to meet the nation's and the world's most urgent needs.

Senator Obama understands that Presidential leadership and federal investments in science and technology are crucial elements in successful governance of the world's leading country. We hope you will join us as we work together to ensure his election in November.

Do remember that my question to CNN involved retaining the USA's status as a scientific superpower.

Following up an earlier item on blaming the poor and minorities for the current financial crisis, Newsweek tackles the argument head-on:

The Community Reinvestment Actapplies to depository banks. But many of the institutions that spurred the massive growth of the subprime market weren't regulated banks. They were outfits such as Argent and American Home Mortgage, which were generally not regulated by the Federal Reserve or other entities that monitored compliance with CRA. These institutions worked hand in glove with Bear Stearns and Lehman Brothers, entities to which the CRA likewise didn't apply. There's much more. As Barry Ritholtz notes in this fine rant, the CRA didn't force mortgage companies to offer loans for no-money down, or to throw underwriting standards out the window, or to encourage mortgage brokers to aggressively seek out new markets. Nor did the CRA force the credit-rating agencies to slap high-grade ratings on subprime debt.

Second, many of the biggest flameouts in real estate have had nothing to do with subprime lending. WCI Communities, builder of highly amenitized condos in Florida (no subprime purchasers welcome there), filed for bankruptcy in August. Very few of the tens of thousands of now-surplus condominiums in Miami were conceived to be marketed to subprime borrowers, or minorities—unless you count rich Venezuelans and Colombians as minorities. The multi-year plague that has been documented in brilliant detail at IrvineHousingBlog is playing out in one of the least subprime housing markets in the nation.

Third, lending money to poor people and minorities isn't inherently risky. There's plenty of evidence that in fact it's not that risky at all. That's what we've learned from several decades of microlending programs, at home and abroad, with their very high repayment rates. And as The New York Times recently reported, Nehemiah Homes, a long-running initiative to build homes and sell them to the working poor in subprime areas of New York's outer boroughs, has a repayment rate that lenders in Greenwich, Conn., would envy. In 27 years, there have been fewer than 10 defaults on the project's 3,900 homes. That's a rate of 0.25 percent.

On the other hand, lending money recklessly to obscenely rich white guys, such as Richard Fuld of Lehman Brothers, or Jimmy Cayne of Bear Stearns, can be really risky. In fact, it's even more risky, since they have a lot more borrowing capacity. And, here, again, it's difficult to imagine how Jimmy Carter could be responsible for the supremely poor decision-making seen in the financial system. I await the Krauthammer column in which he points out the specific provision of the Community Reinvestment Act that forced Bear Stearns to run with an absurd leverage ratio of 33:1, that instructed Bear Stearns hedge-fund managers to blow up hundreds of millions of their clients money, and that required its septuagenarian CEO to play bridge while his company ran into trouble. Perhaps Neil Cavuto knows which CRA clause required Lehman Brothers to borrow hundreds of billions of dollars in short-term debt in the capital markets and then buy tens of billions of dollars of commercial real estate at the top of the market. I can't find it. Did AIG plunge into the credit-default swaps business with abandon because ACORN members picketed its offices? Please. How about the hundreds of billions of dollars of leveraged loans—loans banks committed to private equity firms that wanted to conduct leveraged buyouts of retailers, restaurant companies, and industrial firms? Many of those are going bad now, too. Is that Bill Clinton's fault?

Indeed.

Time mag. asks, and I answer: Palin = disaster

Barack says that Bristol Palin's teenage pregnancy is off-limits:

MONROE, Michigan (CNN) – Barack Obama told reporters firmly that families are off-limits in this campaign, reacting to news that Sarah Palin’s 17-year-old daughter is five months pregnant.

“Let me be as clear as possible,” said Obama, “I think people’s families are off-limits and people's children are especially off-limits. This shouldn't be part of our politics. It has no relevance to Gov. Palin’s performance as governor, or her potential performance as a vice president.”

Obama said reporters should “back off these kinds of stories” and noted that he was born to an 18 year-old mother.

“How a family deals with issues and teenage children, that shouldn't be the topic of our politics and I hope that anybody who is supporting me understands that’s off-limits.”

The Illinois senator became aggravated when asked about rumors on liberal blogs speculating that Palin’s fifth child - Trig - is actually her daughter Bristol’s. A Reuters report Monday quotes a senior McCain aide saying that Obama’s name is in some of posts, “in a way that certainly juxtaposes themselves against their 'campaign of change,’”

“I am offended by that statement,” Obama shot back, not letting the reporter finish his question. “There is no evidence at all that any of this involved us.”

“We don’t go after people’s families,” Obama said. “We don’t get them involved in the politics. It’s not appropriate and it’s not relevant. Our people were not involved in any way in this and they will not be. And if I ever thought that there was somebody in my campaign that was involved in something like that, they’d be fired.”

Although McCain's campaign insists that they knew about this, I remain skeptical, not the least reason being that they're now sending an army of lawyers to Alaska to try to contain this...which is something they should've done beforehand. Time magazine asks whether McCain's pick was "bold or disastrous?" I think that answer is becoming more clear. Let's have a run-down of the woman's baggage:

1. Late addition: She was a member of a fringe Alaskan political group that seeks its independence from the US, and was involved in their 2008 conference
   
2. Late addition: It looks like independent voters are seeing through the nonsense
   
3. She had a shotgun wedding as she got pregnant with her first kid out of wedlock
4. Her husband was arrested on a DWI
5. She's a staunch "abstinence-only" advocate whose teenage daughter got pregnant, the political fallout from which is still to be determined
   
6. Troopergate: She used her authority as governor to try to have her sister's ex-husband fired, then fired his boss when the boss refused, then lied about it [apparently the ex-husband was a dickhead, but the last two points are more important here]
7. She claimed in her first public appearance as VP candidate that she opposed the "Bridge to Nowhere" but this turns out to be a lie, and a bad one, at that
8. She claims to have opposed corruption in Alaska, but said that calling for Ted Stevens resignation would be "premature" after his arrest and received his endorsement, which she paid to run as an ad
9. She directed Ted Stevens' 527 group on his behalf and appeared with him in July after his indictment to appeal for him politically
10. A few months ago, she claims to have no idea what the VP does everyday
    
11. In a 2006 gubenatorial questionaire, she said that she opposed abortions for incest and rape, only giving an exception if it could be proven that the mother might die from childbirth. The Religious Right loves her. Re-read that.
12. From the same source, and many others, she claims that teaching creationism in science classes is the way to go, "teach both."
    
13. On the same anti-science note, she is a global warming denialist
14. She is to the right of McCain on drilling in ANWR, protecting polar bears and protecting the environment in general (yet another anti-science Republican)
15. On the same line of reasoning, she semi-opposed the surge in Iraq, hailed as one of the only things that McCain has not failed at in the past decade or so
16. There is zero national security experience involved in being governor, so quit repeating the "commander-in-chief of the national guard" line. Campbell Brown stumped Tucker Bounds today (H/T: Kos) who tried to equivocate on this -- she didn't command troops to go to Iraq. Not even close. I'm the "commander-in-chief" of my classroom, but that doesn't make me an education policy wonk.
    
17. She is clearly and unequivocally unqualified to be president should something happen to McCain, the oldest presidential candidate ever nominated for a first term whose four bouts with cancer should make everyone think twice

Go Obama-Biden '08! (pic source)

Barack's answers to the Science Debate 2008 questions

I think science is pretty important to the future and direction of our country. The GOP has been waging a war on science for decades, and McCain has continued in that direction with the selection of a creationist champion as VP in Palin.

I've been plugging the Science Debate 2008 for a while, and I noted that Clinton and Obama sent surrogates to the event in February to answer questions while McCain did not. Now Obama's campaign has sent his responses to major scientific issues facing our nation.

In the words of PZ, here are 14 more reasons to support Obama-Biden over McCain-Palin:

[questions in bold]

1. Innovation. Science and technology have been responsible for half of the growth of the American economy since WWII. But several recent reports question America’s continued leadership in these vital areas. What policies will you support to ensure that America remains the world leader in innovation?

Ensuring that the U.S. continues to lead the world in science and technology will be a central priority for my administration. Our talent for innovation is still the envy of the world, but we face unprecedented challenges that demand new approaches. For example, the U.S. annually imports $53 billion more in advanced technology products than we export. China is now the world’s number one high technology exporter. This competitive situation may only worsen over time because the number of U.S. students pursuing technical careers is declining. The U.S. ranks 17th among developed nations in the proportion of college students receiving degrees in science or engineering; we were in third place thirty years ago.

My administration will increase funding for basic research in physical and life sciences, mathematics, and engineering at a rate that would double basic research budgets over the next decade. We will increase research grants for early-career researchers to keep young scientists entering these fields. We will increase support for high-risk, high-payoff research portfolios at our science agencies. And we will invest in the breakthrough research we need to meet our energy challenges and to transform our defense programs.

A vigorous research and development program depends on encouraging talented people to enter science, technology, engineering, and mathematics (STEM) and giving them the support they need to reach their potential. My administration will work to guarantee to students access to strong science curriculum at all grade levels so they graduate knowing how science works – using hands-on, IT-enhanced education. As president, I will launch a Service Scholarship program that pays undergraduate or graduate teaching education costs for those who commit to teaching in a high-need school, and I will prioritize math and science teachers. Additionally, my proposal to create Teacher Residency Academies will also add 30,000 new teachers to high-need schools – training thousands of science and math teachers. I will also expand access to higher education, work to draw more of these students into science and engineering, and increase National Science Foundation (NSF) graduate fellowships. My proposals for providing broadband Internet connections for all Americans across the country will help ensure that more students are able to
bolster their STEM achievement.

Progress in science and technology must be backed with programs ensuring that U.S. businesses have strong incentives to convert advances quickly into new business opportunities and jobs. To do this, my administration will make the R&D tax credit permanent.

2. Climate Change. The Earth’s climate is changing and there is concern about the potentially adverse effects of these changes on life on the planet. What is your position on the following measures that have been proposed to address global climate change—a cap-and-trade system, a carbon tax, increased fuel-economy standards, or research? Are there other policies you would support?

There can no longer be any doubt that human activities are influencing the global climate and we must react quickly and effectively. First, the U.S. must get off the sidelines and take long-overdue action here at home to reduce our own greenhouse gas emissions. We must also take a leadership role in designing technologies that allow us to enjoy a growing, prosperous economy while reducing greenhouse gas emissions by 80 percent below 1990 levels by 2050. With the right incentives, I'm convinced that American ingenuity can do this, and in the process make American businesses more productive, create jobs, and make America’s buildings and vehicles safer and more attractive. This is a global problem. U.S. leadership is essential but solutions will require contributions from all parts of the world—particularly the rest of the world’s major emitters: China, Europe, and India.

Specifically, I will implement a market-based cap-and-trade system to reduce carbon emissions by the amount scientists say is necessary: 80 percent below 1990 levels by 2050. I will start reducing emissions immediately by establishing strong annual reduction targets with an intermediate goal of reducing emissions to 1990 levels by 2020. A cap- and-trade program draws on the power of the marketplace to reduce emissions in a cost- effective and flexible way. I will require all pollution credits to be auctioned.

I will restore U.S. leadership in strategies for combating climate change and work closely with the international community. We will re-engage with the U.N. Framework Convention on Climate Change, the main international forum dedicated to addressing the climate change problem. In addition I will create a Global Energy Forum—based on the G8+5, which includes all G-8 members plus Brazil, China, India, Mexico and South Africa—comprising the largest energy consuming nations from both the developed and developing world. This forum would focus exclusively on global energy and environmental issues. I will also create a Technology Transfer Program dedicated to exporting climate-friendly technologies, including green buildings, clean coal and advanced automobiles, to developing countries to help them combat climate change.

3. Energy. Many policymakers and scientists say energy security and sustainability are major problems facing the United States this century. What policies would you support to meet demand for energy while ensuring an economically and environmentally sustainable future?

America's challenges in providing secure, affordable energy while addressing climate change mean that we must make much more efficient use of energy and begin to rely on new energy sources that eliminate or greatly reduce greenhouse gas emissions. My programs focus both on a greatly expanded program of federally funded energy research and development and on policies designed to speed the adoption of innovative energy technologies and stimulate private innovation.

First, I have proposed programs that, taken together, will increase federal investment in the clean energy research, development, and deployment to $150 billion over ten years. This research will cover:

• Basic research to develop alternative fuels and chemicals;

• Equipment and designs that can greatly reduce energy use in residential and commercial buildings – both new and existing;

• New vehicle technologies capable of significantly reducing our oil consumption;

• Advanced energy storage and transmission that would greatly help the economics of new electric-generating technologies and plug-in hybrids;

• Technologies for capturing and sequestering greenhouse gases produced by coal plants; and

• A new generation of nuclear electric technologies that address cost, safety, waste disposal, and proliferation risks.

I will also work closely with utilities to introduce a digital smart grid that can optimize the overall efficiency of the nation's electric utility system, by managing demand and making effective use of renewable energy and energy storage.

Second, it is essential that we create a strong, predictable market for energy innovations with concrete goals that speed introduction of innovative products and provide a strong incentive for private R&D investment in energy technologies. These concrete goals include:

• Increasing new building efficiency by 50 percent and existing building efficiency by 25 percent over the next decade, and taking other steps that will reduce the energy intensity of our economy 50 percent by 2030;

• Increasing fuel economy standards 4 percent per year and providing loan guarantees for domestic auto plants and parts manufacturers to build new fuel- efficient cars domestically;

• Extending the Production Tax Credit for five years and creating a federal Renewable Portfolio Standard that will require that 10 percent of American electricity be derived from renewable sources by 2012, and 25 percent by 2025; and

• Ensuring that regulations and incentives in all federal agencies support the national energy and environmental goals in ways that encourage innovation and ingenuity.

I will also encourage communities around the nation to design and build sustainable communities that cut energy use with walkable community designs and expanded investment in mass transit.

4. Education. A comparison of 15-year-olds in 30 wealthy nations found that average science scores among U.S. students ranked 17th, while average U.S. math scores ranked 24th. What role do you think the federal government should play in preparing K-12 students for the science and technology driven 21st Century?

All American citizens need high quality STEM education that inspires them to know more about the world around them, engages them in exploring challenging questions, and involves them in high quality intellectual work. STEM education is no longer only for those pursuing STEM careers; it should enable all citizens to solve problems, collaborate, weigh evidence, and communicate ideas. I will work to ensure that all Americans, including those in traditionally underrepresented groups, have the knowledge and skills they need to engage in society, innovate in our world, and compete in the global economy.

I will support research to understand the strategies and mechanisms that bring lasting improvements to STEM education and ensure that promising practices are widely shared. This includes encouraging the development of cutting edge STEM instructional materials and technologies, and working with educators to ensure that assessments measure the range of knowledge and skills needed for the 21st Century. I will bring coherency to STEM education by increasing coordination of federal STEM education programs and facilitating cooperation among state efforts. I recently introduced the "Enhancing Science, Technology, Engineering and Math Education Act of 2008" that would establish a STEM Education Committee within the Office of Science and Technology Policy (OSTP) to coordinate the efforts of federal agencies engaged in STEM education, consolidate the STEM education initiatives that exist within the Department of Education under the direction of an Office of STEM Education, and create a State Consortium for STEM Education. These reforms will strengthen interagency coordination at the federal level, encourage collaboration on common content standards and assessments for STEM education at the state and local levels, and provide a mechanism for sharing the latest innovations and practices in STEM education with educators. I also recently sponsored an amendment, which became law, to the America Competes Act that established a competitive state grant program to support summer learning opportunities with curricula that emphasize mathematics and problem solving.

My education plan is built on the recognition that teachers play a critical role in student learning and achievement. My administration will work closely with states and local communities to ensure that we recruit math and science graduates to the teaching profession. Through Teacher Service Scholarships, a Teacher Residency Program, and Career Ladders, I will transform the teaching profession from one that has too many underpaid and insufficiently qualified teachers to one that attracts the best STEM teaching talent for our schools.

We cannot strengthen STEM education without addressing the broader challenges of improving American education and other priority issues. In addition to a focus on high quality teachers, my comprehensive plan addresses the needs of our most at-risk children, focuses on strong school leaders, and enlists parent and community support. My proposals for a comprehensive “zero to five” program will ensure that children enter school ready to learn. And when they finish school, I will make sure that through the new $4,000 American Opportunity Tax Credit, they will have access to affordable higher education that will provide them with the science fluency they need to be leaders in STEM fields and across broad sectors of our society.

5. National Security. Science and technology are at the core of national security like never before. What is your view of how science and technology can best be used to ensure national security and where should we put our focus?

Technology leadership is key to our national security. It’s essential to create a coherent new defense technology strategy to meet the kinds of threats we may face—asymmetric conflicts, urban operations, peacekeeping missions, and cyber, bio, and proliferation threats, as well as new kinds of symmetric threats.

When Sputnik was launched in 1957, President Eisenhower used the event as a call to arms for Americans to help secure our country and to increase the number of students studying math and science via the National Defense Education Act. That educational base not only improved our national security and space programs but also led to our economic growth and innovation over the second half of the century. Our nation is again hearing a threatening “ping” in the distance, this time not from a single satellite in space but instead from threats that range from asymmetric conflicts to cyber attacks, biological terror and nuclear proliferation. I will lead the nation to be prepared to meet this 21st- century challenge by investing again in math and science education, which is vital to protecting our national security and our competitiveness.

As president I will also ensure that our defense, homeland security, and intelligence agencies have the strong research leadership needed to revitalize our defense research activities and achieve breakthrough science that can be quickly converted into new capabilities for our security.

This year, I was encouraged to see the Department of Defense (DoD) requested a sharp increase in the basic research budget for breakthrough technologies. More is needed. My administration will put basic defense research on a path to double and will assure strong funding for investments in DoD’s applied research programs. We will enhance the connections between defense researchers and their war-fighting counterparts. And, we will strengthen defense research management so that our most innovative minds are working on our most pressing defense problems. A strong research program can also lower procurement costs by reducing technical risks and increasing reliability and performance. Renewing DARPA (the Defense Advanced Research Projects Agency) will be a key part of this strategy.

My administration will build a strong and more productive research program in the Department of Homeland Security (DHS) that will include critical work on cyber and bio security. Because existing programs have been plagued by management problems, we will bring a renewal of talent, organization, and focus, seeking support from our universities, companies, and labs. Another critical role for R&D in national security is energy. Our petroleum dependence continually threatens our security, and my proposals for accelerating new alternative energy technologies will be an important part of my national security R&D agenda.

Finally, we will act to reverse the erosion of the U.S. manufacturing base - which could jeopardize our technical superiority. We need to continue to develop the finest defense systems in the world. But, we are losing domestic production capability for critical defense components and systems. I will implement the recommendations of the Defense Science Board on defense manufacturing, strengthen efforts at DoD’s Manufacturing Technology program, and invest in innovative manufacturing sciences and processes to cut manufacturing costs and increase efficiency.

6. Pandemics and Biosecurity. Some estimates suggest that if H5N1 Avian Flu becomes a pandemic it could kill more than 300 million people. In an era of constant and rapid international travel, what steps should the United States take to protect our population from global pandemics or deliberate biological attacks?

It’s time for a comprehensive effort to tackle bio-terror. We know that the successful deployment of a biological weapon—whether it is sprayed into our cities or spread through our food supply—could kill tens of thousands of Americans and deal a crushing blow to our economy.

Overseas, I will launch a Shared Security Partnership that invests $5 billion over 3 years to forge an international intelligence and law enforcement infrastructure to take down terrorist networks. I will also strengthen U.S. intelligence collection overseas to identify and interdict would-be bioterrorists before they strike and expand the U.S. government’s bioforensics program for tracking the source of any biological weapon. I will work with the international community to make any use of disease as a weapon declared a crime against humanity.

And to ensure our country is prepared should such an event occur, we must provide our public health system across the country with the surge capacity to confront a crisis and improve our ability to cope with infectious diseases. I will invest in new vaccines and technology to detect attacks and to trace them to their origin, so that we can react in a timely fashion. I have pledged to invest $10 billion per year over the next 5 years in electronic health information systems to not only improve routine health care, but also ensure that these systems will give health officials the crucial information they need to deploy resources and save lives in an emergency. I will help hospitals form collaborative networks to deal with sudden surges in patients and will ensure that the U.S. has adequate supplies of medicines, vaccines, and diagnostic tests and can get these vital products into the hands of those who need them.

We also have to expand local and state programs to ensure that they have the resources to respond to these disasters. I will work to strengthen the federal government’s partnership with local and state governments on these issues by improving the mechanisms for clear communication, eliminating redundant programs, and building on the key strengths possessed by each level of government. I introduced legislation which would have provided funding for programs in order to enhance emergency care systems throughout the country.

I will build on America’s unparalleled talent and advantage in STEM fields and the powerful insights into biological systems that are emerging to create new drugs, vaccines, and diagnostic tests and to manufacture these vital products much more quickly and efficiently than is now possible. Unfortunately, the Bush administration has failed to take full advantage of the Bioshield initiative. Because of the unpredictability of the mode of biological attack, I will stress the need for broad-gauged vaccines and drugs and for more agile and responsive drug development and production systems. This effort will strengthen the U.S. biotech and pharmaceutical industry and create high-wage jobs.

7. Genetics research. The field of genetics has the potential to improve human health and nutrition, but many people are concerned about the effects of genetic modification both in humans and in agriculture. What is the right policy balance between the benefits of genetic advances and their potential risks?

The progress that has occurred in genetics over the past half century has been remarkable—from the discovery of DNA’s double helix structure in 1953 to the recent deciphering of all three billion letters of the human genome. New knowledge about genes is already transforming medicine and agriculture and has the potential to change other fields, including energy and environmental sciences and information technology.

I also recognize that the power of modern genetics has raised important ethical, legal, and social issues that require careful study. For example, new developments in human genetics allow individuals to be informed about their risks of various diseases; such information can be useful for diagnosing and treating disease, but it can also be misused by employers or insurers to discriminate. For this reason, I have been a long-time supporter of the recently passed Genetic Information Non-Discrimination Act. In addition, concerned about the premature introduction of genetic testing into the public domain without appropriate oversight, I introduced the Genomics and Personalized Medicine Act of 2007 aimed at ensuring the safety and accuracy of such testing.

Advances in the genetic engineering of plants have provided enormous benefits to American farmers. I believe that we can continue to modify plants safely with new genetic methods, abetted by stringent tests for environmental and health effects and by stronger regulatory oversight guided by the best available scientific advice.

Disease treatment and identification is likewise being transformed by modern genetics. Recombinant DNA (rDNA) technology has produced a number of products such as human growth hormone or insulin or other complicated proteins that are known to be involved in bone metabolism, immune response, and tissue repair. The promise of rDNA is its ability to sidestep potentially harmful intermediaries that could have a pathogenic effect. Some forms of gene therapy-replacing faulty genes with functional copies-in comparison have encountered safety issues that arise from how the functional gene is delivered. As a result, the NIH established the Recombinant DNA Advisory Committee, which now provides advice and guidance on human gene therapy as well as other ethical concerns or potential abuse of rDNA technology. Until we are equipped to ascertain the safety of such methods, I will continue to support the activities and recommendations of the Recombinant DNA Advisory Committee.


8. Stem cells. Stem cell research advocates say it may successfully lead to treatments for many chronic diseases and injuries, saving lives, but opponents argue that using embryos as a source for stem cells destroys human life. What is your position on government regulation and funding of stem cell research?

Stem cell research holds the promise of improving our lives in at least three ways—by substituting normal cells for damaged cells to treat diabetes, Parkinson’s disease, spinal cord injury, heart failure and other disorders; by providing scientists with safe and convenient models of disease for drug development; and by helping to understand fundamental aspects of normal development and cell dysfunction.

For these reasons, I strongly support expanding research on stem cells. I believe that the restrictions that President Bush has placed on funding of human embryonic stem cell research have handcuffed our scientists and hindered our ability to compete with other nations. As president, I will lift the current administration’s ban on federal funding of research on embryonic stem cell lines created after August 9, 2001 through executive order, and I will ensure that all research on stem cells is conducted ethically and with rigorous oversight.

I recognize that some people object to government support of research that requires cells to be harvested from human embryos. However, hundreds of thousands of embryos stored in the U.S. in in-vitro fertilization clinics will not be used for reproductive purposes, and will eventually be destroyed. I believe that it is ethical to use these extra embryos for research that could save lives when they are freely donated for that express purpose.

I am also aware that there have been suggestions that human stem cells of various types, derived from sources other than embryos, make the use of embryonic stem cells unnecessary. I don’t agree. While adult stem cells, such as those harvested from blood or bone marrow, are already used for treatment of some diseases, they do not have the versatility of embryonic stem cells and cannot replace them. Recent discoveries indicate that adult skin cells can be reprogrammed to behave like stem cells; these are exciting findings that might in the future lead to an alternate source of highly versatile stem cells. However, embryonic stem cells remain the “gold standard,” and studies of all types of stem cells should continue in parallel for the foreseeable future.

Rather than restrict the funding of such research, I favor responsible oversight of it, in accord with recent reports from the National Research Council. Recommendations from the NRC reports are already being followed by institutions that conduct human embryonic stem cell research with funds from a variety of sources. An expanded, federally-supported stem cell research program will encourage talented U.S. scientists to engage in this important new field, will allow more effective oversight, and will signal to other countries our commitment to compete in this exciting area of medical research.

9. Ocean Health. Scientists estimate that some 75 percent of the world’s fisheries are in serious decline and habitats around the world like coral reefs are seriously threatened. What steps, if any, should the United States take during your presidency to protect ocean health?

Oceans are crucial to the earth's ecosystem and to all Americans because they drive global weather patterns, feed our people and are a major source of employment for fisheries and recreation. As president, I will commit my administration to develop the kind of strong, integrated, well-managed program of ocean stewardship that is essential to sustain a healthy marine environment.

Global climate change could have catastrophic effects on ocean ecologies. Protection of the oceans is one of the many reasons I have developed an ambitious plan to reduce U.S. emissions of greenhouse gases 80 percent below 1990 by 2050. We need to enhance our understanding of the effect of climate change on oceans and the effect of acidification on marine life through expanded research programs at NASA, the National Oceanic and Atmospheric Administration (NOAA), the National Science Foundation (NSF), and the U.S. Geological Survey (USGS). I will propel the U.S. into a leadership position in marine stewardship and climate change research. Stronger collaboration across U.S. scientific agencies and internationally is needed in basic research and for designing mitigation strategies to reverse or offset the damage being done to oceans and coastal areas.

The oceans are a global resource and a global responsibility for which the U.S. can and should take a more active role. I will work actively to ensure that the U.S. ratifies the Law of the Sea Convention – an agreement supported by more than 150 countries that will protect our economic and security interests while providing an important international collaboration to protect the oceans and its resources. My administration will also strengthen regional and bilateral research and oceans preservation efforts with other Gulf Coast nations.

Our coastal areas and beaches are American treasures and are among our favorite places to live and visit. I will work to reauthorize the Coastal Zone Management Act in ways that strengthen the collaboration between federal agencies and state and local organizations. The National Marine Sanctuaries and the Oceans and Human Health Acts provide essential protection for ocean resources and support the research needed to implement a comprehensive ocean policy. These programs will be strengthened and reauthorized.

10. Water. Thirty-nine states expect some level of water shortage over the next decade, and scientific studies suggest that a majority of our water resources are at risk. What policies would you support to meet demand for water resources?

Solutions to this critical problem will require close collaboration between federal, state, and local governments and the people and businesses affected. First, prices and policies must be set in a ways that give everyone a clear incentive to use water efficiently and avoid waste. Regulations affecting water use in appliances and incentives to shift from irrigated lawns to "water smart" landscapes are examples. Second, information, training, and, in some cases, economic assistance should be provided to farms and businesses that will need to shift to more efficient water practices. Many communities are offering kits to help businesses and homeowners audit their water use and find ways to reduce use. These should be evaluated, with the most successful programs expanded to other states and regions. I will establish a national plan to help high-growth regions with the challenges of managing their water supplies.

In addition, it is also critical that we undertake a concerted program of research, development, and testing of new technologies that can reduce water use.

11. Space. The study of Earth from space can yield important information about climate change; focus on the cosmos can advance our understanding of the universe; and manned space travel can help us inspire new generations of youth to go into science. Can we afford all of them? How would you prioritize space in your administration?

As president, I will establish a robust and balanced civilian space program. Under my administration, NASA not only will inspire the world with both human and robotic space exploration, but also will again lead in confronting the challenges we face here on Earth, including global climate change, energy independence, and aeronautics research. In achieving this vision, I will reach out to include international partners and to engage the private sector to amplify NASA’s reach. I believe that a revitalized NASA can help America maintain its innovation edge and contribute to American economic growth.

There is currently no organizational authority in the federal government with a sufficiently broad mandate to oversee a comprehensive and integrated strategy and policy dealing with all aspects of the government’s space-related programs, including those being managed by NASA, the Department of Defense, the National Reconnaissance Office, the Department of Commerce, the Department of Transportation, and other federal agencies. This wasn’t always the case. Between 1958 and 1973, the National Aeronautics and Space Council oversaw the entire space arena for four presidents; the Council was briefly revived from 1989 to 1992. I will re-establish this Council reporting to the president. It will oversee and coordinate civilian, military, commercial, and national security space activities. It will solicit public participation, engage the international community, and work toward a 21st century vision of space that constantly pushes the envelope on new technologies as it pursues a balanced national portfolio that expands our reach into the heavens and improves life here on Earth.

12. Scientific Integrity. Many government scientists report political interference in their job. Is it acceptable for elected officials to hold back or alter scientific reports if they conflict with their own views, and how will you balance scientific information with politics and personal beliefs in your decision-making?

Scientific and technological information is of growing importance to a range of issues. I believe such information must be expert and uncolored by ideology.

I will restore the basic principle that government decisions should be based on the best- available, scientifically-valid evidence and not on the ideological predispositions of agency officials or political appointees. More broadly, I am committed to creating a transparent and connected democracy, using cutting-edge technologies to provide a new level of transparency, accountability, and participation for America’s citizens. Policies must be determined using a process that builds on the long tradition of open debate that has characterized progress in science, including review by individuals who might bring new information or contrasting views. I have already established an impressive team of science advisors, including several Nobel Laureates, who are helping me to shape a robust science agenda for my administration.

In addition I will:

• Appoint individuals with strong science and technology backgrounds and unquestioned reputations for integrity and objectivity to the growing number of senior management positions where decisions must incorporate science and technology advice. These positions will be filled promptly with ethical, highly qualified individuals on a non-partisan basis;

• Establish the nation’s first Chief Technology Officer (CTO) to ensure that our government and all its agencies have the right infrastructure, policies and services for the 21st century. The CTO will lead an interagency effort on best-in-class technologies, sharing of best practices, and safeguarding of our networks;

• Strengthen the role of the President’s Council of Advisors on Science and Technology (PCAST) by appointing experts who are charged to provide independent advice on critical issues of science and technology. The PCAST will once again be advisory to the president; and

• Restore the science integrity of government and restore transparency of decision- making by issuing an Executive Order establishing clear guidelines for the review and release of government publications, guaranteeing that results are released in a timely manner and not distorted by the ideological biases of political appointees. I will strengthen protection for “whistle blowers” who report abuses of these processes.

13. Research. For many years, Congress has recognized the importance of science and engineering research to realizing our national goals. Given that the next Congress will likely face spending constraints, what priority would you give to investment in basic research in upcoming budgets?

Federally supported basic research, aimed at understanding many features of nature— from the size of the universe to subatomic particles, from the chemical reactions that support a living cell to interactions that sustain ecosystems—has been an essential feature of American life for over fifty years. While the outcomes of specific projects are never predictable, basic research has been a reliable source of new knowledge that has fueled important developments in fields ranging from telecommunications to medicine, yielding remarkable rates of economic return and ensuring American leadership in industry, military power, and higher education. I believe that continued investment in fundamental research is essential for ensuring healthier lives, better sources of energy, superior military capacity, and high-wage jobs for our nation’s future.

Yet, today, we are clearly under-investing in research across the spectrum of scientific and engineering disciplines. Federal support for the physical sciences and engineering has been declining as a fraction of GDP for decades, and, after a period of growth of the life sciences, the NIH budget has been steadily losing buying power for the past six years. As a result, our science agencies are often able to support no more than one in ten proposals that they receive, arresting the careers of our young scientists and blocking our ability to pursue many remarkable recent advances. Furthermore, in this environment, scientists are less likely to pursue the risky research that may lead to the most important breakthroughs. Finally, we are reducing support for science at a time when many other nations are increasing it, a situation that already threatens our leadership in many critical areas of science.

This situation is unacceptable. As president, I will increase funding for basic research in physical and life sciences, mathematics, and engineering at a rate that would double basic research budgets over the next decade.

Sustained and predictable increases in research funding will allow the United States to accomplish a great deal. First, we can expand the frontiers of human knowledge. Second, we can provide greater support for high-risk, high-return research and for young scientists at the beginning of their careers. Third, we can harness science and technology to address the “grand challenges” of the 21st century: energy, health, food and water, national security, information technology, and manufacturing capacity.

14. Health. Americans are increasingly concerned with the cost, quality and availability of health care. How do you see science, research and technology contributing to improved health and quality of life?

Americans have good reasons to be proud of the extraordinary role that medical science has had in combating disease, here and throughout the world, over the past century. Work sponsored by the National Institutes of Health (NIH), other government agencies, and our pharmaceutical and biotechnology industries has produced many vaccines, drugs, and hormones that have improved the quality of life, extended life expectancy, and reduced the dire consequences of many serious illnesses and disabilities. These advances include methods for preventing and treating coronary artery disease and stroke, which have reduced mortality rates by two-thirds; new drugs and antibodies that allow us to effectively treat certain cancers; anti-viral agents that allow most patients with AIDS to control their disease; drugs that often help make severe psychiatric illnesses manageable; and new vaccines that are reducing the incidence of virus-related cancers; and minimally invasive surgery techniques that reduce hospitalizations, complications, and costs. We can expect much more from the exciting biomedical research now underway. For example, we can foresee medical care that will allow physicians to tailor care to individual patients, matching therapies to those most likely to benefit.

However, today our citizens have understandable concerns about their ability to afford the care they need, especially when our underlying system of paying for health care is broken. We spend more on health care per capita than people of other countries, yet lower income groups continue to suffer significant disparities in both access to care and health outcomes. Without major changes, costs will continue to increase. Our population is aging, many cancers and chronic disorders remain difficult to treat, and there are continuing threats of new and re-emerging infectious diseases.

It's wrong that America's health care system works better for insurance and drug companies than it does for average Americans, who face skyrocketing health care costs. My plan makes health care more secure and affordable by strengthening employer-based coverage, protecting patients' ability to choose their own doctors, and saving families $2,500 dollars by requiring insurance companies to cover prevention and limiting excessive insurance company charges. My plan covers everybody by requiring insurance companies to cover pre-existing conditions, providing tax credits to small businesses and working families, and covering all uninsured children.

These are difficult problems, and science and technology can solve only some of them. The effectiveness of medical care can be improved, and its costs can be reduced, by greater emphasis on best practices, electronic medical records, hospital safety, preventive strategies, and improved public health surveillance. The increased investments I support for medical research at the NIH may yield discoveries that reduce the cost of drug development, and we may produce new methods to prevent diseases that are costly to treat. But efforts to control costs also should make greater use of the tools for prevention and clinical management that already exist; enlist more effective participation of the Centers for Disease Control (CDC) and the Food and Drug Administration (FDA), as well as the NIH; and encourage investments in healthcare and health research by the private and not-for-profit sectors.

Overall, I am committed to three major tasks that will be necessary to confront widespread concerns about the nation’s health: provision of healthcare plans to all of our citizens; comprehensive efforts to make our health care system more cost-efficient; and continued biomedical research to understand diseases more thoroughly and find better ways to prevent and treat them.

I'll update when and if McCain's camp responds and try to analyze the differences.

Confused about coffee?

I have been before. Is it good for you to drink it, or not? Decaf only? How many cups a day?

Here are your answers.

Summary: drinking 3 cups a day or less of regular coffee may actually be good for you in many ways.

Comment on "Extraordinary Claims Demand Extraordinary Evidence"

We've heard the phrase before that evidence ought to be inversely proportional to the ordinariness of a claim: the more ordinary, the less evidence we require for tentative belief; the less ordinary, the more evidence we require for belief. This seems a wise maxim to hold, no matter the area of espistemology. Many theists, though, toss this maxim out the window when discussing the paucity of evidence they rely upon (Scripture) to justify belief in the most extraordinary of all claims (miracles).

I just left the following comment at an old haunt of mine:

If something occurs that is outside of not only my own personal experience, but the cumulative experience of science, especially since science exists to test boundaries and conditions to see what the laws of nature are and when/if they change, much skepticism should be brought to bear on the claim.

I would say it is a good deal simpler than you are making it here, and perhaps this could be seen more clearly if we remove the context from "miracle" to "violation" of the laws of nature. Suppose that I, scientist X, am working under conditions that no one has worked under before: say, a particle accelerator of potential 20 TeV. If I see something under those conditions that "appears" to violate the laws of physics, the same amount of scrutiny should be brought to bear on my claim as any other claim that a violation has occurred, be it of divine origin or not. And the purpose of the doubt here is to actually find out the truth: the verification principle in the philosophy of science. If the claim is true, and if the violation is natural, then the conditions and test may be repeated and ought to produce the same "violation": at which time, and once fully described, it no longer is a violation, but another law of nature!

On the other hand, suppose that we aren't discovering new laws of nature by creating conditions and tests which are extraordinary, but rather we're in the realm of the mundane. In these conditions, a supposed violation would probably draw just as much scrutiny from you (a believer) as from me (an unbeliever). If I claim that I have a dragon in my shed (to use Sagan as you did in your post), for instance, you would be naturally skeptical and would require more evidence than my "say-so" about it. But if I claim to have a lawn mower in my shed, you won't even blink.

Ditto with religion: the issue is not whether or not a God logically could violate the laws of nature, but whether the evidence we have (the say-so of anonymous persons 2000 years ago) is enough to convince us that violations did happen.

Spirituality and drugs

Back when I was running Gator Freethought (AAFSA at the time), I was often pressed for creative material to use at our non-guest-speaker meetings. At one meeting, I decided to talk about the role of drugs in so-called "spiritual" or transcendent experiences, and especially drugs like psilocybin, after reading about it at world-science.net that previous week. The meeting went fairly well, I guess, although I admittedly wasn't as prepared as I should have been.

The long story short is that some drugs (especially psilocybin) seem to induce a state of mind akin to what Buddhist monks enter when they go into transcendental meditation, in that one loses all sense of self and an indelible sense of oneness with the cosmos emerges. That's also the report from a few friends of mine who have experimented with mushrooms.

Anyway, I was reminded of that as I read that in studies on those exposed to psilocybin, the effects on their mood and happiness have lasted a very long time -- over a year. Since my pipe dreams still include the FBI/CIA thing, I will hold off until that ship sails. After that, I think I'd like to see what transcendent experiences I can have with psilocybin.

Summary of origin of life research

I like to write things about abiogenesis. Go here for some great peer-reviewed publications on the origin of the genetic code and the evolution of the chemical processes underlying metabolism.

In a reply to Gordy Slack, Nick Matzke wrote something great at the Panda's Thumb on the same topic and I want to paste in the relevant portion below:

Origin of Life (OOL)

Slack lists a “few worthy points” creationists make. Here is the first:

First, I have to agree with the ID crowd that there are some very big (and frankly exciting) questions that should keep evolutionists humble. While there is important work going on in the area of biogenesis, for instance, I think it’s fair to say that science is still in the dark about this fundamental question.

Minor point first: Shallit points out that “biogenesis” means production of life from life, whereas Slack is talking about the origin of life (OOL). Oops.

Major points: PZ says that sure, big exciting unanswered questions like the origin of life exist in science, but scientists said this first, and furthermore consider them research opportunities, not flaws. Shallit separates OOL from evolution, specifying that evolution is what occurs after you have life; Shallit does this in the face of Slack asserting that this response is disingenuous. Shallit also argues a little over whether or not we’ve made only “little progress” in understanding the OOL, but says even if we’ve only made a little progress, it’s better than ID.

This mini-debate points out what I think, and have often said in conversations, is a major flaw in how we respond to creationists. All too often, when the OOL comes up in popular discussions (reporters, online debates, etc.), the anti-creationist will reply with some variation of “sure, it’s a tough unsolved problem, but we’re working on it”, or the wizened statement “actually, the OOL is outside of the domain of evolutionary biology”, or finally, “we’re pretty much in the dark about the OOL, but at least what we have is better than the creationists giving up and saying a miracle occurred.”

My take: It is high time all of these statements be discarded or highly modified. They are basically lazy, all-too-easy responses relying on hair-splitting technicalities or nearly philosophical assertions of the “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” variety. And the worst part is that these sorts of statements mis-describe the actual state of the science among the people who work in the field. It is simply not true that we, the scientific community, know almost nothing about the OOL (what an individual who spent a career working on fossils or fruit flies or speciation might know personally is a different question).

Here is a short list of things we have discovered or confirmed in the last 50 years or so pertaining to the origin of life. In my opinion all of these points have reached high enough confidence that they are unlikely to change much with future discoveries, and our confidence in them does not depend in uncertainties in the remaining unanswered questions.

OOL Discovery #1. All known life can be traced back to a single common ancestor which, compared to what most people think of as present-day life (i.e. plants and animals), was relatively simple – microscopic, single-celled, perhaps as complex as an average bacterium or perhaps somewhat less so.

Because a lot of creationists, and sometimes others, are a bit thick in the head on correctly understanding this point, let me bash away at some common misconceptions. The phrase “single common ancestor” does not, and never has for people who were paying close attention, referred to a literal single individual organism. Think about a phylogenetic tree with humans and chimps on the branches. When you trace the tree back to the “common ancestor” of chimps and humans, does that node represent a literal single individual? No, of course not! Everyone (well, everyone paying attention) realizes that that ancestral node represents a species or population sharing genes in a gene pool. Ditto for all of the other ancestral nodes in a phylogenetic tree, including the Last Common Ancestor of known life.

With this understood, the debate initiated by Ford Doolittle and others over the precise nature of the Last Common Ancestor – they argue that it was a population of unicells that were rampantly trading genes – can be put in the correct context. It’s basically a debate about how wide or narrow the bottleneck the Last Common Ancestor represents, and whether (for example) modern life might contain some genes derived by lateral transfer from pre-LCA lineages that are now extinct. These debates are fascinating and highly technical, but they don’t undermine at all Point #1. Somewhat ironically and counterintuitively, those who say that there was rampant lateral transfer – this is supposed to be the “radical” position that “uproots the Tree of Life” when its proponents get their blood up – are actually pushing the LCA to something more and more like a traditional gene pool, i.e. species, i.e. what every other node in a phylogenetic tree represents.

Any way you slice it, all known life (with minor derived exceptions, and excepting viruses) shares a suite of protein and RNA genes, a DNA-RNA-protein system and a mostly standard genetic code (again with minor derived exceptions), etc. Even if various other bits of modern life came from other ancestral lineages (unlikely for most features in my opinion but there may be some exceptions), this shared system indicates that all known life, i.e. all the stuff that’s not extinct, descends from a pretty good bottleneck where these features were fixed in the “population.” And this reconstructed ancestor is maybe as complex as a typical bacterium and probably less so. It could be that in the last 50 years science discovered that known life had for-real multiple origins, or that at the root of the tree was a complex multicellular organism with 30,000 genes and huge, elaborately regulated, genome, but instead we get a unicell with a relatively small & simple genome. Various caveats, important to scientists but irrelevant to beginner-level education and dealing with creationists (e.g., somewhat more genes may have been passed through the bottleneck in some but not all organisms if the LCA was more of a gene-trading community) should not be allowed to distract from the Main Point: science has confirmed the hypothesis, going back at least to Darwin, that the ancestor of modern life was much less complex than life today.

OOL Discovery #2. The Last Common Ancestor itself was the product of evolution from an even simpler ancestor. The simplest piece of evidence for this is that a number of the genes found in the Last Common Ancestor are homologous, thus derived from a single common ancestor by duplication and modification. An example is the F1Fo-ATPase of bacteria, which interconverts proton gradients (or sometimes sodium ion gradients, which are chemically very similar) and ATP, the main energy currency of cells. It has relatives in all branches of life: the V1Vo-ATPases in eukaryotes (and some prokaryotes), and the A1Ao-ATPases of archaea, and phylogenetic analysis indicates that this membrane-embedded system was found in the LCA (this also confirms that the LCA had membranes, which is useful although already very likely on multiple grounds).

Anyway, the bit of the V/F/A-ATPases that deals with ATP is a heterohexamer, i.e. complex of six proteins (that’s the “hexamer” bit) of two different types (thus “hetero”), cleverly named alpha and beta. The alphas and betas alternate in the six-protein ring, and the betas interact with ATP. The key point here is that the alpha and beta subunits share statistically strong sequence similarity. The simple explanation is that the heterohexamer was descended from a homohexamer made up of six identical proteins forming a ring. Thus we know – as strongly as we know that two people are related by ancestry based on DNA sequence similarity – that long before the last common ancestor of life there was a cellular organism that had something like the F1Fo-ATPase, but a simpler version with a homohexameric ATPase complex instead of a heterohexamer.

This may seem like a trivial point by itself but it is just an example; there are dozens, perhaps hundreds, of others. The evolution of ATPases can be traced much further back: the next closest relative is a homohexamer found in, of all things, the core of the bacterial flagellum and the nonflagellar type 3 secretion systems. Thus the V/F/A-ATPases and the flagellar/nonflagellar type 3 secretion systems can be traced back to an ancestral membrane-associated complex with multiple shared proteins (because the V/F/A-ATPases and type 3 secretion systems shared not just the ATPase protein but also an associated external stalk protein, FliH/Fo-b, which by the way is something I pretty much predicted in 2003 in the Big Flagellum Essay and which Mark Pallen and colleagues nailed down for real in the peer-reviewed literature in 2006).

Even more distant relatives are known: the homohexameric rho (involved in bacterial RNA processing) and homohexameric RecA (DNA processing). And there are even more distant hexameric sister groups; the whole related set of proteins is known as the AAA ATPases if you want to look them up. And if memory serves there are yet more distant non-hexameric relatives.

In other words, the Last Common Ancestor had a suite of ATPase proteins which had already evolved from a single protein ancestor by duplication and divergence events which are still strongly statistically detectable in the present day. And there are a number of other genes for which the same can be said, and undoubtedly many others which occurred but are not statistically detectable billions of years later due to the decay of the signal.

So far we’ve established that anyone, creationist, evolutionist, or whomever, who says that the scientific understanding of the origin-of-life is chemicals –> mystery –> modern-complexity life doesn’t know the first thing about what they’re yapping about. At the very least we’ve got chemicals –> mystery –> quite simple precursor to the LCA –> LCA –> modern life. But there is yet more that we know

OOL Discovery #3. DNA/RNA/protein-based life was preceded by something even simpler, an RNA world or at least an RNA-heavy world.

The RNA world has gotten better press attention than OOL Discoveries #1 and #2 so I will spend less time on it. Read the wikipedia page for an introduction and particularly the EvoWiki page for some of the main supporting evidence.

There are two points worth making about the RNA world that should be made every time this issue is discussed in popular or remedial creationism-related discussions. First: there was a time, not too long ago, when the fact that DNA coded for proteins, and proteins were necessary for making DNA, seemed like the ultimate intrinsically unsolvable problem in the study of the origin of life. It’s the ultimate chicken-and-egg problem, or, if you like, the ultimate “irreducible complexity” problem. And yet, scientists worked on it for a few decades and discovered a workable, surprisingly simple solution.

Second, surprisingly enough (well, surprising to creationists or the naive), this solution, the RNA world, hasn’t just sat around as a purely theoretical just-so story. A highly productive research program has been built on the RNA World concept. Areas that have experienced substantial success in the last decade or two include: the discovery of increasingly diverse catalytic capabilities of RNA; the evolution new capabilities in replicating, evolving RNAs; the evolution of the genetic code which translates DNA to RNA to protein; and the prebiotic origin of RNA components.

Each of these areas has developed into a subfield which has experienced major research discoveries in recent years. For example, on the origin of the genetic code, this paper assembles dozens of indicators on the order in which amino acids were added, step-by-step, to the genetic code and shows that the evidence strongly supports a fairly specific scenario (which shares many similarities with early, more speculative scenarios built on the basis of just a few lines of evidence).

Ergo, we don’t just know that the Last Common Ancestor of Life was simple, and that it’s ancestor was simpler, and that it’s ancestor was an even simpler RNA-dominated critter; we even have a decent idea about the order of the steps by which the genetic code itself evolved.

OOL Discovery #4. The increasingly simple ancestors of modern life weren’t made out of just anything, they were made out of chemicals that just happen to be generated by plausible abiotic mechanisms found in early solar systems. This area is also better known, but many, both creationists and scientists and journalists who haven’t thought about it enough, tend to think of prebiotic chemistry as the beginning and ending of origin-of-life studies, and for some extremely foolish reason which I can’t fashion, probably simple carelessness, tend to think that until chemists pop life out of a test tube then we “know nothing” about the origin of life.

Here’s a short list of discoveries about prebiotic chemistry, all of which increase our confidence in the idea that the origin of life was a gradual process, from abiotic chemicals to simple replicators to the simple ancestors of modern life which were discovered above. I’ll include some subtleties that I’ve seen lead people astray on occasion.

* Water is one of the most common compounds in the universe, and was/is common in the solar system (subtlety: most of it is frozen, but remember that on any planet with hot stuff inside and cold frozen stuff outside will have a just-right region in-between where water will be liquid)

* Earthlike planets are likely reasonably common (subtlety: we haven’t discovered them directly yet, but this is isn’t because they aren’t there, it’s because our instruments are at present only sensitive enough to detect big, close-in planets around other stars. Nevertheless, the distribution of the stuff we can detect strongly indicates that there are plenty of earthlike planets in earthlike orbits which will be discoverable in the near future. That’s a prediction, scientists will test it, that’s science for you. Remember that back in the 1990s, ID proponent William Dembski was skeptical of the whole idea of extrasolar planets. Whoops!)

* Amino acids are easy to generate by a variety of processes, and this is not only supported by experiment, but by observation of amino acids in meteorites and other extra-terrestrial material. (Subtlety: There is a body of serious scientific thought which suggests that the Earth’s early atmosphere was more neutral and less reducing than was thought a few decades ago, but (1) this isn’t for sure, the redox chemistry of the Earth’s rocks and atmosphere is a complex business (and I wonder if the impact which produced the moon, removing much of the mantle but leaving the Earth enriched in heavy iron might have made the Earth’s atmosphere more reducing, at least early on – comments?); (2) even in a neutral atmosphere/ocean system there will be locally reducing conditions – heck, there are local reducing conditions here on earth right now even with our heavily oxidized crust and atmosphere; (3) as it turns out, even neutral atmospheres can produce amino acids in respectable yields anyway; and (4) this whole sub-debate is somewhat moot since we have direct evidence of amino acids forming in the solar system e.g. in meteorites.)

* RNA precursors are somewhat tougher, but there has been progress in that area also, and anyway there is no requirement that the first replicator must have been RNA; various other simpler “worlds” have been suggested and are being explored (PNA, peptide nucleic acids; other NAs of various sorts; and lipid worlds, which have the distinct charm of instant replication ability and statistical inheritance, with daughter bubbes containing a subsample of the chemicals making up the mother bubbles, and growth occuring by incorporation of lipids from the environment and other bubbles; so maybe the first “replicators” were even simpler than some have thought).

* The main energy source of present life is ATP and other energized phosphate molecules. So, what was the prebiotic source of those? It turns out that inorganic polyphosphates (chains like phosphate-phosphate-phosphate-phosphate) have energetic bonds very similar to those of ATP (which is adenine-phosphate-phosphate-phosphate), and yet can be formed by the simple heating of certain rocks.

* Less well-known is the fact that prebiotic origins of many cofactors and other universal small biotic compounds have also been reconstructed

What is actually being worked on. The above should convince you that the idea that we know nothing or very little about the OOL is just uninformed foolishness. The field has made major progress. There are some famous puzzles remaining, but they do not add up to “we know nothing about the origin of life.” Furthermore, some of the puzzles that creationists, and sometimes others, consider to be major hangups, are not necessarily so. For example:

* The origin of chirality (the left-handedness of amino acids). This is a major puzzle if you make the extremely foolish and unthinking assume (like creationists do, but sometimes others) that the first use of amino acids in early life was supposed to be in long amino acid chains made up of 100+ amino acids randomly assembled from an even mixture of 20+ different amino acids with an even mixture of right- and left-handed amino acids. But over here in the real world, where the origin of the genetic code has been reconstructed in some detail, we know the following: the first primitive genetic code used just one or a few amino acids, and one of the first was glycine, which is the simplest amino acid, the most common amino acid produced in prebiotic experiments, and which is achiral (no left-hand/right-hand difference) to boot. If, as has been proposed, the first use of amino acids was as something relatively prosaic, i.e. a short chain of hydrophobic residues to insert into an early membrane, then (a) the odds of getting 10 or so amino acids at once that were either left-handed or glycine were not small at all, and (b) it wouldn’t have mattered much if the occasional right-handed amino acid was incorporated, because the crude chemical property of hydrophobicity is all that is really important, and (c) therefore the origin of a preferred chirality could have been more or less random. There is some very interesting work indicating that nature has various processes which might increase the proportion of left-handed amino acids, but it’s not at all clear that these will be necessary to explain chirality.

* The origin of the first replicator. This really is the big cahuna of the OOL discussion, and where the big and contentious debates are still occurring within science, but again I find that many discussants operate with very crude and naive assumptions about what early replicators “should” have been like and what prebiotic experiments “should” be able to produce to “solve” this problem. It’s a mini-version of the “produce a modern cell in a test tube for me or you haven’t solved the OOL” silliness, i.e., “produce a self replicating RNA World, with duplicating ‘informational genetic sequences’ in the test tube, and until you do you can’t say we know anything about the origin of replicators.”

Again, over here in reality-land the distinctions between replicators and nonreplicators are not so clear. I have already mentioned “lipid-world” ideas and the concept of “statistical inheritance”, where overall chemical properties are transmitted or accumulated, without the need for exact inheritance of a sequence. Similar concepts have been applied by OOL workers to amino acid and nucleic acid “sequences”, where before exact inheritance of sequence is acheived, there might have been a stage where inexact incorporation of a range of chemically similar bases was occurring.

Another subtlety is the difference between “self-replication” and processes where prebiotic compounds go through a series of chemical processes, and differences in chemical kinetics increase the frequency of compounds that have more rapid kinetics; if these compounds are auto-catalytic, they can begin a feedback system where chemicals with higher kinetics take over in a proto-selection system. Strangely, although everyone who takes college chemistry learns that the product of chemical reactions is a combination of thermodynamics and kinetics, many discussions of the OOL from scientists, and all of the derivative critiques by creationists, have focused on thermodynamics. This is particularly odd since self-replication is the ultimate example of kinetics overwhelming thermodynamics.

What’s the point of this sub-discussion? Well, if it is the case that the origin of the first “replicator” was, like everything else we’ve discovered in the study of OOL, a slow, gradual (meaning step-by-step), cumulative process, then it is pretty foolish to have in our heads the idea that OOL experiments should produce full-on replicators in one go to be successful experiments. This is basically a strawman expectation that expresses conceptual confusion about what an evolutionary origin of life “should” look like.

(As an aside, I think biology education would be a lot better off if the above points were consistently made in science curricula and textbooks at the high school and college level. Teaching OOL as a story from simple to complex, rather than a detective story from complex to simple, is probably a mistake if the goal is to get students to understand why scientists think the way they do about these issues.)

The Main Point

Now that we’ve briefly reviewed the OOL field and discussed the major discoveries and some of the common misconceptions, let’s return to the statements I quoted at the beginning. Is it really true that “science is still in the dark” on the OOL, as Slack said? Not a chance. If we lived in a world where it actually looked like the first living things were as complex or more complex than life today, or where the last common ancestor contained absolutely no evidence of an evolutionary history, or where big obvious puzzles like the interdependency of DNA/RNA/protein had no hint of solution, or where the building blocks of life were completely unrelated to those produced in prebiotic experiments – all of these things would be true, say, on a robotic planet without microscopic life, where robots were replicated by macroscopic assembly performed by other robots, and powered by hooking up to a grid of fusion-fueled power plants – then we could say “science is still in the dark” on the origin of this robotic biosphere. But instead, we have numerous lines of evidence all pointing towards the notion that current life descends from a relatively simple ancestor, and that ancestor descends from a series of even simpler ancestors. Why should any of this evidence exist, if life was poofed into existence all in one step, which is what the creationists/IDers think happened even when they won’t admit it, because they are not brave enough to defend what they actually think? Additionally, why should the remaining puzzles, particularly about the origin of the first replicator, cause any unusual amount of discomfort for scientists? Whether or not that puzzle is solved, the gap between prebiotic experiments and the first replicators (or better yet, pseudoreplicators with statistical inheritance) is a drastically reduced vestige of a gap compared to what the gap looked like in, say, 1950. When you think about it, the creationists’ attempt to insert miraculous divine intervention into this tight little gap which is left is actually pitiful, and a pretty sad commentary on the state that creationism/ID has been reduced to. The verse “And God said, let the NA precursors link together into a short noncoding kinetically favored chain and pseudoreplicate approximately statistically after their kind” just doesn’t have the same ring to it.

Similarly, if my characterization of the state of the science is accurate, then it is highly irresponsible for scientists to address creationist arguments about the origin of life with statements like, “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” or “actually, the OOL is outside of the domain of evolutionary biology.” The first statement surrenders without argument a favorite bogus creationist talking point, and so confirms and passes on their misinformation, even if the evolution “wins” the argument in his own head on some broader philosophical point. Instead of putting the creationist back on his heels with a wave of contradictory evidence, that sort of response, even if the philosophical point is valid, leaves the creationist and any of his sympathetic readers irate that the empirical point is not being addressed, and that the creationist/ID position is being excluded by the rules of the game. The fact that this sort of response is a lot easier and faster to put together does not make it the best one.

The second statement, splitting the OOL from evolutionary theory, is only technically correct in a sort of legalistic, hairsplitting way. Sure, it’s true that technically, “evolution” only happens once you have life, or at least replicators, but getting from replicators to the last common ancestor is most of what most people think about when they’re thinking about the origin of life, i.e., “where did the evolutionary ancestor of all life today come from?” and all of that is evolution all the way. Furthermore, even the origin of the first classical “replicator” was itself very likely an evolutionary process, in that it occurred in stepwise fashion and not all-at-once, and that the first replicator was likely preceded by various sorts of pseudoreplication, statistical inheritance and kinetic biases. If you remove evolution from your thinking about the origin of the first replicator then it is very likely you will never understand how it happened, or what the current research on the question is about. Finally, even apart from these detailed considerations, “evolution” reasonably has a broader meaning – the evolution of the universe, the solar system, the planet, and the planet’s geochemistry, and the origin of life and the origin of the first replicator must be understood as part of that larger evolutionary history.

One other telling point is that the statement “but the OOL is outside of evolutionary theory” response also has the problem of simply dodging the hard work of describing the discoveries and work of modern science, a problem I have already described. In conclusion, if it were up to me, I would completely scrap this statement from the rhetorical toolkit of evolution defenders.

The OOL topic turned into an essay on its own, but we still have another few of Slack’s points to address.

An excellent summary, if I may say so. He left out a few things that I've mentioned before, like the discovery of the role of borate in natural ribose synthesis by a colleague of mine at UF, and upstairs neighbors, Alonso Ricardo and Fabianne Frye. Go here for some great peer-reviewed publications on the origin of the genetic code and the evolution of the chemical processes underlying metabolism.