Spore and Evolution

 
Spore is a computer game that let's you "evolve" organisms beginning with a simple cell and moving "upwards" to creatures that can build spaceships. The game is designed by Will Wright whose previous credits include SimCity and The Sims.

Wright and his company have been heavily promoting the game as a way of learning about evolution. As part of this promotion they have distributed free copies to many scientists in advance of the opening day of sales in retail stores. Here's how it's described on the Spore Website.

How will you create the universe?

With Spore you can nurture your creature through five stages of evolution: Cell, Creature, Tribe, Civilization, and Space. Or if you prefer, spend as much time as you like making creatures, vehicles, buildings and spaceships with Spore’s unique Creator tools.

CREATE Your Universe from Microscopic to Macrocosmic - From tide pool amoebas to thriving civilizations to intergalactic starships, everything is in your hands.

EVOLVE Your Creature through Five Stages - It’s survival of the funnest as your choices reverberate through generations and ultimately decide the fate of your civilization.

Time for a reality check. Spore is a computer game. It's purpose is to make bundles of money for Will Wright and his company. It may be an excellent game but it is NOT a way of learning about evolution. Evolution does not have a purpose or a direction.

Carl Zimmer has just published an article in The New York Times about Spore and computer simulations [Gaming Evolves]. Some scientists don't think the game reflects evolution.

Unlike the typical shoot-them-till-they’re-all-dead video game, Spore was strongly influenced by science, and in particular by evolutionary biology. Mr. Wright will appear in a documentary next Tuesday on the National Geographic Channel, sharing his new game with leading evolutionary biologists and talking with them about the evolution of complex life.

Evolutionary biologists like Dr. Near and Dr. Prum, who have had a chance to try the game, like it a great deal. But they also have some serious reservations. The step-by-step process by which Spore’s creatures change does not have much to do with real evolution. “The mechanism is severely messed up,” Dr. Prum said.

Nevertheless, Dr. Prum admires the way Spore touches on some of the big questions that evolutionary biologists ask. What is the origin of complexity? How contingent is evolution on flukes and quirks? “If it compels people to ask these questions, that would be great,” he said.

The object of the game is to "evolve" advanced creatures that the player "designs." What are the chances that the average player is going to appreciate the roles of contingency, and quirks? Probably so close to zero that it's not worth discussing.

I have a problem when we talk about games like Spore and real evolution in the same breath. I have a problem when someone like Will Wright is promoted on the National Geographic TV channel. The press release from National Geographic sounds ominous ..

(WASHINGTON, D.C. — AUGUST 21, 2008) In the newest creation from Electronic Arts Inc. (EA) and video game pioneer and "The Sims" mastermind Will Wright, Spore™ enables players to design a virtual galaxy of new life, such as a one-eyed web-footed creature with a snout, and then control their species' evolution. But how much real-world science is behind this groundbreaking new game? And what genetic connections do people share with a universe of strange organisms?

On Tuesday, Sept. 9, at 10:00 p.m. ET/PT, National Geographic Channel (NGC) presents the premiere of How to Build a Better Being, the companion documentary to the highly anticipated new video game Spore, which will be released nationally on Sunday, Sept. 7. The show, which is also included in the limited run of the collectable "Spore Galactic Edition," joins Wright and leading scientists in exploring the genetic information we share with all animals — even creatures we could never have envisioned. From prehistoric fish with wrists to 8-ton elephants with trunks, get powerful new insight into the origin of species and how our prized parts came to be. Then see how evolutionary creature-making is translated into a brave new world of gaming.

"What are the things that evolution has at its disposal to define a creature, to mix and match the parts, and eventually come up with a unique organism that's going to live its life and try to reproduce?" — Will Wright, gaming innovator

Some would argue that anything that promotes evolution is a step in the right direction. It's a valid point.

But why can't we have our cake and eat it too? Why can't we promote evolution but do it in a scientifically accurate manner? It's abundantly clear to all scientists that the general public knows little about evolution and what little they know is mostly wrong. Do we have to cater to those false impressions?

What effect is it going to have in the long run if we misrepresent science by pretending that evolution is progressive and ladder-like and leads eventually to us—or at least leads to intelligent animals? Is anyone else concerned about this?

The video clip below doesn't mention Spore. It looks like the same old evo-devo emphasis on semi-conserved regulatory genes and regulation of animal development as keys to understanding how humans evolved.


The Spore advertisement exploits the National Geographic connection.

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Comment Policy on Sandwalk

 
I think it's time to re-state my policy on comments. I don't like censorship. That's why my policy is close to the one mockingly described at Draft Blogger's Code of Conduct.

We also decided we needed an "anything goes" badge for sites that want to warn possible commenters that they are entering a free-for-all zone. The text to accompany that badge might go something like this:

"This is an open, uncensored forum. We are not responsible for the comments of any poster, and when discussions get heated, crude language, insults and other "off color" comments may be encountered. Participate in this site at your own risk."

As a consequence of this policy, there are several very annoying people making comments on Sandwalk. I don't respond to comments from those people but others are free to do so.

There are two types of comments that will be removed from Sandwalk. These are cases where censorship is justified, in my opinion.

The first is outright spam of the sort that we all have to tolerate from time to time. If your comment serves no other purpose than to direct people to 30 different "free" travel websites, for example, then these comments will be quickly removed.

The second is blatant promotion of commercial products on the pretext that they are relevant to the content of a posting. An example of the second type is the posting of a website for collagen creme in the comments section of an article about the biochemistry of collagen.

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Alternating Generations

 
Check out When Ferns Don't Look Like Ferns by Christopher Taylor on Catalogue of Organisms. The concept of alternating generations is an important concept that everyone should understand.

All plants undergo alternation of generation to a greater or lesser degree. Here's an interesting way to think about the concept from the Biology course notes at the University of Miami.

If animals were to undergo alternation of generations, then imagine that you are the diploid individual (sporophyte). Your mother, the gametophyte, would be haploid, and would look completely different from you (maybe like a SmurfTM). Your grandmother would be diploid, and look like you. Your own offspring would look like your mama the SmurfTM, your grandchildren would look like you, and so on.

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[Image Credit: Lewis & Clark]

Genes and Geography

 
Your DNA tells you who you are related to. This has led to projects that can trace your ancestors. Your DNA can also tell you where you've come from. This is because most of our ancestors didn't get out much. They tended to marry their cousins and close neighbors. Over many generations the people in a particular region came to resemble each other much more closely than they resembled people in other countries.

Razib at Gene Expression has been discussing the evolutionary implications of this kind of population genetics. See his latest posting and learn how to interpret the map shown below [Genetic map of Europe; genes vary as a function of distance].

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Monday's Molecule #86

 
In honor of all those students who are returning to college this week's molecule is another simple one that should be familiar to every undergraduate taking an introductory biochemistry course. Your task is to identify the molecule and give me its correct common name—the one required on an exam—and the complete, correct IUPAC name.

There's a direct connection between today's molecule and a Nobel Prize. We are looking for the single person most responsible for identifying this molecule as an important part of a metabolic pathway. This person didn't know the exact structure but got the basic chemistry correct. Be careful, there are several possible candidates who haven't already been featured on Sandalk. I want the one person who best meets the criterion.

The first person to correctly identify the molecule and name the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

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

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are no open.

UPDATE: The molecule is ATP of adenosine 5′-triphosphate. Lots of people got the molecule but nobody guessed the Nobel Laureate (Hans von Euler-Chelpin). There are no winners this week.

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What the Heck?

 
Coturnix posted a video on A Blog Around the Clock. His posting, entitled Just replace '9/11' with 'POW'..., was critical of McCain and his running mate Sarah Palin. The main issue in the election, according to Coturnix and others, is race. If true, that's sad.

I tried to watch the video that Coturnix embedded in his blog and this is what I get ...


Isn't that interesting? Is this a joke or has the server at hulu has been set up to recognize and block IP numbers that are registered outside of the USA? Why?

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Why Is Canada in Afghanistan?

 
The Toronto Star asked this question a few days ago. Here's the entire article from Our Man in Afghanistan. I've chosen to accompany it with a photograph of the Prime Minister of Canada shaking hands with Hamid Karzai. This is the same photo that Canadian Cynic used in Sorry ... why exactly are we over there again?.

My words fail. So here's Britain's The Independent:

"The Afghan president, Hamid Karzai, has pardoned three men who had been found guilty of gang raping a woman in the northern province of Samangan.

The woman, Sara, and her family found out about the pardon only when they saw the rapists back in their village.

“Everyone was shocked,” said Sara’s husband, Dilawar, who like many Afghans uses only one name. “These were men who had been sentenced and found guilty by the Supreme Court, walking around freely.”

Sara’s case highlights concerns about the close relationship between the Afghan president and men accused of war crimes and human rights abuses.

The men were freed discreetly but the rape itself was public and brutal. It took place in September 2005, in the run up to Afghanistan’s first democratic parliamentary elections.

The most powerful local commander, Mawlawi Islam, was running for office despite being accused of scores of murders committed while he had been a mujahedeen commander in the 1980s and a Taliban governor in the 1990s, and since the fall of the Taliban in 2001. Sara said one of his sub-commanders and body guards had been looking for young men to help in the election campaign.

“It was evening, around the time for the last prayer, when armed men came and took my son, Islamuddin, by force. I have eye-witness statements from nine people that he was there. From that niGht until now, my son has never been seen.”

Dilawar said his wife publicly harangued the commander twice about their missing son. After the second time, he said, they came for her. “The commander and three of his fighters came and took my wife out of our home and took her to their house about 200 metres away and, in front of these witnesses, raped her.”

Dilawar has a sheaf of legal papers, including a doctors’ report, which said she had a 17mm wound in her private parts cut with a bayonet. Sara was left to stumble home, bleeding and without her trousers."

Remind me again what Canadians are getting killed and mutilated for?

Exactly. All we're doing is propping up a government that's as corrupt as the group we are fighting. We are caught in the middle of a civil war and the best thing to do is to get the heck out and let the Afghans sort it out for themselves.

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Science and Public Relations

 

I have come to this conclusion: the greatest tragedy of public polity, in science and without, in the democratic nations, one that looks very likely to me to be the major proximal cause of the ultimate failure of democracy, is the invention of public relations.

Read more from John Wilkins at Spin versus framing: the tragedy of PR.

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Barack Obama Answers Science Questions

 
An organization called Science Debate 2008 has crafted 14 questions about science for the US Presidential candidates. Barack Obama has submitted his answers [Presidential answers to the top 14 science questions facing America].

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?

... 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.

I'm a little confused about how the American system of government works. I think the answer means the following: "My administration will submit to Congress a proposal to increase funding ..." Is that correct? Is it just campaign rhetoric when a Presidential candidate talks like this or does the President really have more power to make laws than I imagine?

The second part of his answer suggests that the office of the President will somehow influence the granting agencies to direct more of their funds to early-career researchers and to "high-risk, high-payoff" grant applications. Can the White House make NIH, for example, distribute money differently or does that require legislation to enact?

I don't think anyone believes that Barack Obama wrote these answers, although I'm certain that he approved them. It would be interesting to know who did write the response and how much influence that person(s) will have if Obama wins the election in November. Does anyone know who his advisers are?

The answers don't seem to be much different than those I would have expected from most other Democratic candidates, or from John Kerry in 2004, or Al Gore in 2000. Am I missing something or is there some radical change in the way things are going to be done in Washington that escapes me?¹

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1. Doubling of research funding in 10 years means a yearly increase of 8%. While this is better than an increase that doesn't match inflation, it doesn't strike me as a very radical proposal to fix the funding situation.

[Hat Tip: Jim Lippard]

Genomics and Darwinism!?

 
The scientific research journal Genome Research is proposing to publish a special issue on "Genomics and Darwinism" to coincide with Darwin's 200th birthday [Genome Research].

Genome Research is now accepting submissions for a special issue, entitled Genomics and Darwinism, devoted to comparative and evolutionary genomics, including primary research reporting novel insights in large-scale quantitative and population genetics, genome evolution, and natural and sexual selection.

The deadline for submissions is September 1 and the issue is expected to coordinate with Darwin's 200th birthday (and 150th anniversary of the publication of On the Origin of Species) in February 2009.

The creationists have already jumped on this as evidence that "Darwinism" is the proper terminology when referring to evolution: see DaveScot's post on Uncommon Descent entitled Is “Darwinism” a term only used by creationists?.

I wish that Genome Research had used "Genomics and Evolution" as their theme. Or, even better, "Genomics: Beyond Darwinism." Is this what Carl Zimmer warned us about when he said that he feared an over-emphasis on Darwin [Carl Zimmer at Chautauqua]? I think Carl is right and I think we need to push back. I'll be sending a letter to the editors of Genome Research.

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Dealing With the Controversy

 
Here's an exercise for those of you who are truly interested in teaching accurate science. Go to the recent posting by Casey Luskin on Evolution: News & Views and figure out how to respond to his challenge. He's claiming that a great deal of evolution is "random" but that's not what the "Darwinists" are saying ["Random" Samples of Media and Textbook Descriptions of Darwinian Evolution].

Is he right?¹ What should we teach in school?

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1. Yes, and no. As usual Casey Luskin has only a superficial understanding of evolution and a very weak grasp of reality. However, from time to time he accidentally stumbles onto an important point. Let's set aside the fact that he has no idea what he's talking about and address how we should respond to such criticisms. My view is here: [Evolution by Accident].

Tangled Bank #112

 
The latest issue of Tangled Bank has been published on Science Notes [Tangled Bank #112].

Welcome, science readers, to Tangled Bank 112. It’s a privilege to host so much good science writing. Today’s entries are presented mainly with only the authors’ comments because it’s late and I want to get them published.

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If you want to submit an article to Tangled Bank, send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Connie Barlow and Michael Dowd at Chautauqua

 
One of the many highlights of my week at Chautauqua was meeting Connie Barlow and her husband Michael Dowd. Michael is the author of Thank God for Evolution. His blog, The Evolutionary Evangelist promotes the concept of Evolution Theology ....

As I and others are now using the term, Evolution Theology, or Religion 2.0, refers to those whose position on the science vs. religion controversy tends toward reconciliation or synthesis. The term points broadly to those who do not see themselves at either end of the polarized debate as it is currently framed (either anti-evolutionary creationism and intelligent design at one end, or anti-religious atheism at the other). Theistic evolutionists, religious naturalists, evolutionary humanists, emergentists, pantheists, panentheists, theosophists, and the 11,000+ signers of the Clergy Letter Project may differ in how they integrate evolution and theology , but they all do.

The short Wikipedia article on Michael Dowd refers to him as an itinerant Pentecostal preacher. He and his wife travel around America promoting evolution and Christianity. Michael and Connie sat in on a class that I took (Evolution and Christianity). Michael's version of Christianity is very confusing to me, as was the instructor's version. It's part of the so-called "sophisticated" Christianity that seems to deny any scientifically detectable evidence of God's intervention in affairs of the natural world. Undetectable, that is, unless you are a person of faith. People of faith can see the hand of God in events such as the breakup of the Soviet Union and the tearing down of the Berlin wall whereas the rest of us see these as entirely natural events. People who hold this position often go as far as saying that they really don't believe in supernatural beings because God is everywhere in nature.

I had never heard of Michael Dowd before last week but I have been a fan of Connie Barlow for fifteen years. She is the author of two books that I consult frequently when discussing evolution. The first one is From Gaia to Selfish Genes: Selected Writings in the Life Sciences published in 1991 and the second is Evolution Extended: Biological Debates on the Meaning of Life published in 1995.


The books are collections of excerpts from publications by leading thinkers about evolution. The selection is excellent. All the important ideas are there. In some cases this is my primary source because I haven't been able to find the original works; for example, I don't have a copy of The Logic of Life by François Jacob.

It was a delight to finally meet Connie Barlow (and you, too, Michael!). I wish I had known that she would be in Chautatuqua so I could have brought my books for her to sign. As you might have guessed, Connie is the "evolution" part of the team while Michael is the "theology" part. The unusual part of this relationship is that Connie doesn't necessarily buy into religion in the same way as her husband.

Connie published another book in 2002 called The Ghosts Of Evolution Nonsensical Fruit, Missing Partners, And Other Ecological Anachronisms. I'm not familiar with this book but I think I'll buy it.

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Useful RNAs?

The latest issue of Nature contains a news feature by Anna Petherick [Genetics: The production line]. The article is mostly about a new regulatory RNA called HOTAIR but it's the implications of this discovery that bother me.

Let's look at the question being posed ...

If more than 90% of the genome is 'junk' then why do cells make so much RNA from it?

One of the answers being promoted by many molecular biologists is that this RNA is mostly functional and it represents a massive new level of control that has hitherto gone unnoticed. That doesn't mean that we never knew about regulatory RNAs because, in fact, we've known about them for over three decades. The important point of this opinion is that these RNAs are abundant and it "explains" the presence of so much non-coding DNA in eukaryotic genomes.

The other answer to the question is that transcription is sloppy and it frequently makes mistakes. That's why there's a very low level of transcription from all parts of the genome. It's junk RNA. This explanation seems to be widespread in the molecular biology community but it doesn't get much press because there are few papers that discuss this hypothesis [What is a gene, post-ENCODE?] [Junk RNA].

The probem in this field is that it's difficult to publish a paper that proves a negative (but see Brosius (2005)) and it's easy to publish a paper showing that a particular non-coding RNA has a function. The rare examples of those with function get all the publicity and obscure the fact that 99% of these transcripts may not have a function.

The article continues with ...

It is hard to comprehend the upheaval that RNA has been causing in molecular biology over the past few years. Once viewed as a passive intermediary, it was thought to faithfully carry genetic messages from the DNA sequence to the protein-making machinery, where things were made that actually got things done. Biologists were comfortable in the knowledge that only 1–2% of the human genome made protein-coding RNA in this way, and most of the rest was filler. So when, in 2005, geneticist Thomas Gingeras announced that some cells churn out RNA molecules from about 80% of their DNA, he astonished scientists attending the Biology of Genomes meeting at Cold Spring Harbor Laboratory in New York. Why should cells bother with so much manufacturing if, as it seemed, such a tiny fraction was involved in the important business of protein-making?

I wasn't at this meeting but I'd be very surprised if the scientists were "astonished." I'm pretty sure most of them thought that this was an artifact of some kind, probably due to accidental transcription.

This is a case where the author of the article could have benefited from interviewing more of the skeptics.

Over the past three years or so the case for this 'pervasive transcription' has strengthened. The phenomenon has now been ascribed to mice, fruitflies, nematode worms and yeast. These studies, and Gingeras's original reports, came from microarrays — a technology that relies on the tendency of nucleic acids to find their complementary cousins in a solution. Gingeras works for the microarray manufacturer Affymetrix in Santa Clara, California. But not everyone has been persuaded of the extent of pervasive transcription, in part because microarrays are subject to background 'noise'. Even using no RNA, control chips will give off some signals, and results can be a matter of interpretation.

Yes, false positives may account for some of the observations but I think most scientists recognize that the microchips are actually detecting rare transcripts. The question is whether these rare transcripts are biologically significant or whether they are artifacts like most of the alternative splice variants that made all the headlines a few years ago.

If the transcripts are accidental and nonfunctional then the fact that we see this in mice, fruit flies, nematodes, and yeast isn't a surprise. It is not evidence that the transcripts are functional. We would like to see evidence that most of these transcripts are (1) evolutionarily conserved, (2) reproducibly synthesized from a functional promoter, and (3) abundant enough in vivo to make a difference,

John Mattick, the director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia, has no such qualms. He is a long-time advocate of non-coding RNA's importance. The doubters, he says, "keep regressing to the most orthodox explanation [that the long RNAs are junk]. But they can't just sit on their intellectual backsides and tell us to prove it."

John Mattick is one of the most vocal cheerleaders for non-coding RNA. He maintains that huge amounts of it are biologically functional. His statement is a tacit confession that he has no proof of his claims. What in the world is wrong with asking for "proof" (evidence) whether sitting on our backsides or standing?

Is Mattick advocating science by assertion? It certainly seems that way in many of his papers.

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Brosius, J. (2005) Waste not, want not – transcript excess in multicellular eukaryotes. Trends in Genetics 21:287-288 [DOI: 10.1016/j.tig.2005.02.014]

Everyone Must Read this Paper

 
Christopher Taylor writes on Catalogue of Organisms ...

Nearly thirty years ago, a paper was published that almost every student of evolutionary science will end up reading at some point in their career. Despite being only eighteen pages long and containing no original research, many people see it as marking something of a revolution in biology.

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