Monday's Molecule #134: Winner

 
The technique is partition chromatography. The example shown below could be either thin layer chromatography or paper chromatography. The principle is the same. It is nicely explained by Bill Chaney of the University of Nebraska Medical Center. Unfortunately for him, there were others who responded faster, although not as eloquently.

The technique you are referring to is partition chromatography. The sample is spotted at one end of the immobile phase and a liquid mobile phase is allowed to adsorb along the phase, often in an enclosed container, which is an necessity if the mobile phase is a mixture of volatile liquid. Because different molecules have varying affinities for the solid and mobile phases (their partition coefficient) they are carried along the direction of the flow of the mobile phase at different rates giving their Rf value. The immobile phase can be paper, thin layers of different compounds like silica gel, or ion exchange resins. It is also used in Gas Liquid and Gas Solid chromatography as well where the mobile phase is a gas.

The Nobel Laureates are Martin and Synge for inventing partition chromatography. The winner is Maria Altshuler of the University of Toronto. Congratulations Maria, you beat out a dozen others who had the right answer!

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Today's "molecule" isn't a molecule. I'm looking for the technique that's illustrated by the example shown here. Describe the technique and identify the Nobel Laureates who discovered it.

The first person to identify the technique and the Nobel Laureates, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only two ineligible candidates for this week's reward: Alex Ling of the University of Toronto, and Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

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

Correct responses will be posted tomorrow.

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

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The image is taken from this website on paper chromatography.

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Did Life Arise 3.5 Billion Years Ago?

J. William Schopf is a paleontologist at the University of California, Los Angeles (USA). He became famous in the 1990s for his studies of the Apec chert—ancient rocks in the northern part of Western Australia near the town of Marble Bar. Parts of these rocks have been reliably dated to 3.465 billion years ago.

Schopf claimed to have discovered bacteria fossils in these rocks. He published his results in a highly cited Science paper back in 1993 (Schopf, 1993). The title of the paper "Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life" establishes his claim.

It's worth quoting the abstract of the paper because it shows the confidence Schopf exuded. Not only did he claim that the 3.5 billion year old Apex chert contained bacterial fossils but, even more astonishingly, he identified eleven different species and clearly stated that they resembled cyanobacteria.

Eleven taxa (including eight heretofore undescribed species) of cellularly preserved filamentous microbes, among the oldest fossils known, have been discovered in a bedded chert unit of the Early Archean Apex Basalt of northwestern Western Australia. This prokaryotic assemblage establishes that trichomic cyanobacterium-like microorganisms were extant and morphologically diverse at least as early as approximately 3465 million years ago and suggests that oxygen-producing photoautotrophy may have already evolved by this early stage in biotic history.

The data were immediately challenged. There were two problems, First, many paleonotologists questioned whether the "fossils" were really fossils. They suggested that the structures could easily be inorganic in nature and not remnants of living organisms. Secondly, the presence of cyanobacteria—among the most complex bacteria—is inconsistent with molecular data. Even though the early tree of life is complicated, the available evidence indicates that cyanobacteria arose late in the evolution of bacterial taxa. It's very unlikely that the earliest forms of life could be cyanobacteria, or even photosynthetic bacteria.

The publicity associated with the presumed discovery of the earliest forms of life was too much to resist. In spite of the criticisms, the "fact" of these "fossils" made it into the textbooks within months of the discovery. The original figures have often been purged from more recent editions but the widespread claim that life originated 3.5 billion years ago persists.

Schopf defended and promoted his work in a trade book—The Cradle of Life— published in 1999. In that book he appeared to address most of his critics. He insisted that his "fossils" met all the rigorous tests of science.

The Fossils Aren't Fossils

Over the years, the challengers became more and more emboldened. In 2002 Martin Brasier published a re-analysis of Schopf's original fossils and noticed that the published images were not as complete as they could be. In the figure shown here, Brasier et al. (2002) compare Schopf's original images ("b" and "c") with a larger view of the same material.

The "fossils" look much more like inorganic inclusions that just happen to resemble strings of bacteria, according to Brasier. A debate between Martin Brasier and Bill Schopf took place in April 2002 and it was widely perceived to have resulted in victory for Brasier. The "fossils" aren't fossils.

A report in Nature presented the bottom line (Dalton, 2002).

The textbooks say that oxygen-producing microorganisms evolved some 3.5 billion years ago. But as that claim and its author come under attack, the history of life on Earth may have to be rewritten...

Supporters and critics of Schopf alike describe him as a driven and tenacious character — nicknamed 'Bull' Schopf by some — whose energy and enthusiasm has done much to raise the profile of micropalaeontology, and to draw funding into the field. "He has a driving ambition to be in the limelight, and he doesn't like to admit he's wrong," says one former colleague. But these traits have led Schopf into conflict with his collaborators on at least one previous occasion.

A similar piece in Science helps drive the point home (Kerr, 2002).

The search for fossils in rocks formed before the Cambrian explosion of life 540 million years ago "has been plagued by misinterpretation and questionable results," leading paleontologist William Schopf of the University of California, Los Angeles (UCLA), once noted. Now Schopf's own claim for the oldest known fossils--fossils that have entered textbooks as the oldest ever found--is under attack as a misinterpretation of intriguingly shaped but purely lifeless minerals.

A paper in this week's issue of Nature argues that the microscopic squiggles in a 3.5-billion-year-old Australian chert are not fossilized bacteria, as Schopf claimed in a 1993 Science paper (30 April 1993, p. 640), but the curiously formed dregs of ancient hot-spring chemistry. "There's a continuum [of putative microfossils] from the almost plausible to the completely ridiculous," says lead author Martin Brasier, a micropaleontologist at the University of Oxford, U.K. "Our explanation is that they are all abiogenic artifacts."

If true, the analysis calls into question the fossil record of life's first billion years. It would also raise doubts about the judgment of Schopf, the man chosen by NASA to set the standard for distinguishing signs of life from nonlife at the press conference unveiling martian meteorite ALH84001 (Science, 16 August 1996, p. 864). But Schopf says that such speculation is unwarranted. "I would beg to differ" with Brasier's interpretation, he says. "They're certainly good fossils."

The latest paper by Pinti et al. (2009) extends earlier observations of the Apex chert that re-interpret it as a hydrothermal vent. Temperatures reached 250° during formation of the vent and the alternation between molten and cooler forms of material was not conducive to life. Furthermore, deposits of iron oxides and clay minerals could be mistaken for microfossils .

Organic Traces of Early Life?

One of the early signatures of life is trace organic matter. In theory, it is possible to distinguish between organic molecules that form by chemical processes and organic molecule that are synthesized by living organisms. The key is the ratio of the two isotopes of carbon; ¹²C and ¹³C. The common isotope is ¹²C and living organisms preferentially incorporate ¹²C when they synthesize carbohydrates, lipids, and other molecules of life.

The result is that organic molecules made in cells have a smaller percentage of the heavy isotope, ¹³C. The presence of "lighter" organic molecules is evidence of life—or so the story goes.

Even this evidence of early life is being challenged. For example, a review of the evidence for life in the 3.7 billion year old rocks of western Greenland points out two potential problems (Fedo et al., 2006). First, the material has probably been misidentified—it is not what it was claimed to be. Recent evidence suggests that the rocks are igneous, not sedimentary. Secondly, the isotope ratios may not be accurate and/or they can be explained by non-biological processes. Isotope ratios are not an unambiguous indication of life.

These problems, and others, with the Akilia rocks of western Greenland have been known for many years. They were discussed in a hard-hitting Nature News and Views article by Stephen Moorbath in 2005. You may not understand the technical details (I don't) but there's no mistaking the tone when Moorbath says ...

This persuasive discovery seems an almost inevitable, yet highly problematic, consequence to the increasing scientific doubts about the original claim. We may well ask what exactly was the material originally analysed and reported? What was the apatite grain with supposed graphite inclusions that figured on the covers of learned and popular journals soon after the discovery? These questions must surely be answered and, if necessary, lessons learned for the more effective checking and duplication of spectacular scientific claims from the outset.

To my regret, the ancient Greenland rocks have not yet produced any compelling evidence for the existence of life by 3.8 billion years ago. The reader is reminded that another debate on early life is currently in progress on 3.5-billion-year-old rocks in Western Australia, where chains of cell-like structures, long identified as genuine fossils10, have recently been downgraded by some workers11 to the status of artefacts produced by entirely non-biological processes. To have a chance of success, it seems that the search for remnants of earliest life must be carried out on sedimentary rocks that are as old, unmetamorphosed, unmetasomatized and undeformed as possible. That remains easier said than done. For the time being, the many claims for life in the first 2.0–2.5 billion years of Earth's history are once again being vigorously debated: true consensus for life's existence seems to be reached only with the bacterial fossils of the 1.9-billion-year-old Gunflint Formation of Ontario12.

There's another, potentially more serious, problem with using isotope ratios as evidence of early life. Gérard et al. (2009) have recently documented the presence of modern bacteria in drillcore samples of rocks that are 2.7 billion years old. They detected trace amounts of ribosomal RNA that were sufficient to identify more that ten diverse species of bacteria living in these subsurface formations.

If modern bacteria can invade and colonize ancient rocks then it's highly likely that more ancient bacteria can also live in ancient rocks. Over the course of millions of years, these colonizers can leave traces of organic molecules. But those molecules do not show that life existed in those places at the time when the rocks were formed. In other words, just because you have "light" organic molecules in rocks that are billions of years old does not mean that the cells that created those molecules lived billions of years ago.

The conclusion of the Gérard et al. (2009) paper is worth quoting,

Our results strongly suggest that contemporary bacteria inhabit what are generally considered exceptionally well-preserved subsurface Archaean fossil stromatolites of the Hamersley Basin, Western Australia. They are possibly in very low numbers, their distribution confined to microfractures where water may circulate (perhaps only intermittently), and their metabolic activities might be extremely low. However, upon geological timescales spanning 2.7 Gy, even such low cell numbers must have contributed significantly to the pool of biogenic signatures associated to these rocks, including microfossils, biological isotopic fractionation and lipid biomarkers. Although our results do not necessarily invalidate previous analyses, they cautiously question the interpretation of ancient biomarkers or other life traces associated to old rocks, even pristine, as syngenetic biogenic remains when bulk analyses are carried out.

What does all this tell us about early life? It tells us that the evidence for life before 3 billion years ago is being challenged in the scientific literature. You can no longer assume that life existed that early in the history of Earth. It may have, but it would be irresponsible to put such a claim in the textbooks without a note of caution.

What else does this story tell us? It tells us something about how science is communicated to the general public. The claims of early life were widely reported in the media. Every new discovery of trace fossils and trace molecules was breathlessly reported in countless newspapers and magazines. Nobody hears about the follow-up studies that casts doubt on those claims. Nobody hears about the scientists who were heroes in the past but seem less-than-heroic today.

That's a shame because that's how science really works. That's why science is so much fun.

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Brasier, M.D., Green, O.R., Jephcoat, A.P., Kleppe, A.K., Van Kranendonk, M.J., Lindsay, J.F., Steele, A., and Grassineau, N.V. (2002) Questioning the evidence for Earth's oldest fossils. Nature 416::76-81. [PubMed]

Dalton, R. (2002) Microfossils: Squaring up over ancient life. Nature 417:782-784. [doi:10.1038/417782a]

Fedo, C.M., Whitehouse, M.J. and Kamber, B.S. (2006) Geological constraints on detecting the earliest life on Earth: a perspective from the Early Archaean (older than 3.7 Gyr) of southwest Greenland. Phil. Trans. R. Soc. B 361:851-867. [doi: 10.1098/rstb.2006.1836]

Gérard, E., Moreira, D., Philippot, P., Van Kranendonk, M.J., and López-García, P. (2009) Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia. PLoS ONE 4: e5298. [doi:10.1371/journal.pone.0005298]

Pinti, F.L., Mineau, R., and Clement, V. (2009) Hydrothermal alteration and microfossil artefacts of the 3,465-million-year-old Apex chert. Nature Geoscience 2:640-643. [doi: 10.1038/ngeo601]

Schopf, J.W. (1993) Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science 260:640-646. [PubMed]

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Gérard, E., Moreira, D., Philippot, P., Van Kranendonk, M., & López-García, P. (2009). Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005298

Pinti, D., Mineau, R., & Clement, V. (2009). Hydrothermal alteration and microfossil artefacts of the 3,465-million-year-old Apex chert Nature Geoscience, 2 (9), 640-643 DOI: 10.1038/ngeo601

Human Y Chromosome Mutation Rates

 
One thing men are really good at is making mistakes—just ask any woman. When it comes to mutations we are ten times better than women at ensuring the evolution of the species.

Knowing the actual rate of mutation in humans—or any other species—is important for many reasons. For one thing, it tells us about the maximum possible rate of evolution. For another, it gives us an important clue about the differences between beneficial, detrimental, and neutral alleles.

It's a lot more difficult to measure mutation rates than you might imagine. In theory, you could sequence the genomes of hundreds of parents and their offspring and identify mutations that must have occurred in the germ lines of the parents. In practice, this is far too expensive and time-consuming and, besides, it will miss any severely detrimental mutations.

But let's say you did the experiment in spite of the time and money. If the measured mutation rate turned out to be close to the calculated value, then you could assume that most of the mutations were neutral. A few might be beneficial.

Another possibility is to measure the number of differences between two individuals who are separated by a large number of generations. In this case you are measuring the combined effect of mutation and the fixation of alleles in a population. This is what we do whenever we compare gene sequences from different species.

Alleles can be fixed by natural selection or by random genetic drift. If most are fixed by natural selection (adaptation) then you'll learn very little about the overall mutation rate aside from a minimum estimate. That's because you don't know the fitness of every allele and how fast it became fixed in the population and you don't know how many mutations were detrimental or neutral, and what happened to them.

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.

Motoo Kimura (1968)
However, you have a fighting chance if most mutations give rise to neutral alleles. In that case, the overall rate of fixation by random genetic drift is the same as the mutation rate [see: Random Genetic Drift and Population Size]. The data suggest that this is the correct scenario. When we compare individual genes from different species, the observed differences are consistent with the expected result if most of the differences are due to the fixation of neutral alleles by random genetic drift.

For the comparison between humans and chimpanzees, the estimated rates are remarkably consistent. They range from about 2 × 10^-8 to about 5 × 10^-8 mutations per nucleotide (base pair) per generation (Nachman, 2004; Britten, 2002). This agrees with the known error rate of DNA replication, which is about 10^-10 per nucleotide per replication. Since there are about 400 DNA replications between the male zygote and mature sperm, this translates to 4 × 10^-8 mutations per nucleotide per generation [see, Mutation Rates].

This is where men come in. There are many fewer cell divisions in the female line—about 30—so the egg contributes fewer mutations than the sperm. In fact, for most purposes we can ignore women in these calculations. Men have another big advantage. They have a Y chromosomes that's passed down directly from father to son and it doesn't recombine with any female chromosomes.¹ You don't need to worry about fixation.

If you sequence Y chromosomes from related men you can get a direct estimate of the mutation rate provided most of the alleles are neutral. It's best to choose men who are distantly related since there won't be many differences between closely related men. Two sons, for example, are likely to have identical Y chromosomes.

Xue et al. (2009) did the experiment [Human mutation rate revealed]. They sequenced the Y chromosomes of two men who were separated by 13 generations. After eliminating repetitive regions, the relevant region of comparison was 10.15 × 10⁶ nucleotides (base pairs, 10.15 Mb). The men differ at four confirmed sites. This gives a mutation rate of 3.0 × 10^-8 per generation or 0.75 × 10^-10 per nucleotide per DNA replication.

The agreement is remarkable. What this means is that we have a good handle on the mutation rate in humans and we have growing evidence that most mutations are neutral (i.e. most of our genome is junk).

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1. This isn't strictly correct but you can ignore the small regions where recombination is possible.

Britten, R.J. (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Nat. Acad. Sci. USA 99:13633-13635. [doi: 10.1073/pnas.172510699]

Nachman, M.W. (2004) Haldane and the first estimates of the human mutation rate. J Genet. 83:231-233. [PubMed]

Xue, Y., Wang, Q., Long, Q., Ng, B.L., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., Zhao, Y.; Asan, Macarthur, D.G., Quail, M.A., Carter, N.P., Yang, H., Tyler-Smith, C. (2009) Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Curr Biol. Aug 26. [Epub ahead of print] [doi: 10.1016/j.cub.2009.07.032]

Xue, Y., Wang, Q., Long, Q., Ng, B., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., & Zhao, Y. (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree Current Biology DOI: 10.1016/j.cub.2009.07.032

Proof of Special Creation

 
I'm sure many of you were troubled by the argument of Rev. William A. Williams who wrote The Evolution of Man Scientifically Disproved. As I explained in a previous posting, Rev. Williams has proved by mathematics that evolution cannot account for the current population of the Earth. There should be 2 × 10³⁷³ people if evolution is true [The Evolution of Man Scientifically Disproved].

We take comfort in the fact that this disproof is not widely known. But that's about to change. A reader¹ alerted me to a YouTube video where a renowned Mathematics Professor explains the disproof in a manner that any creationist idiot can understand.

Now that it's on YouTube, everyone's going to know about it. Evolution is in big trouble.

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1. Thank-you.

Monday's Molecule #134

 
Today's "molecule" isn't a molecule. I'm looking for the technique that's illustrated by the example shown here. Describe the technique and identify the Nobel Laureates who discovered it.

The first person to identify the technique and the Nobel Laureates, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only two ineligible candidates for this week's reward: Alex Ling of the University of Toronto, and Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

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

Correct responses will be posted tomorrow.

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

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The image is taken from this website on paper chromatography.

Get a Ph.D.!!!

 
I already have a degree but for those of you who don't, here's a golden opportunity.

Now you can get real degree just in 4-5 weeks on base of your professional experience

We will get your self a verifiable degree of:
Masters, Bachelors and PhD

Ring right now

1.305.460.5721

Leave your msg, with your full name and number and we will get back to you shortly.

I think it refers to science and engineering degrees. English doesn't seem likely to be one of the eligible categories for Ph.D. studies.

I don't know why it takes so long to get a Bachelor or a Masters degree. Surely you can do it in less time than it takes to get a Ph.D.? Maybe it's cheaper to get a B.Sc. or an M.Sc. The email message didn't mention anything about the cost of the degrees—I'm guessing it would be about 30,000 rubles.

The "personal experience" part is intriguing. Ms. Sandwalk wants to know if you can get a Ph.D. for 35 years of putting up with Ph.D.'s. And I want to know if you can get one for 35 years of putting up with ....... never mind.

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Creation

 
The film Creation is being shown at the upcoming Toronto International Film Festival [Creation]. One of the viewings is at Roy Thompson Hall at 8PM on Thursday, Sept. 10. Anyone interested?

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Capitalism

 
I think I'll be going to see this movie. Don't get me wrong, I'm a fan of Michael Moore but that doesn't mean I agree with everything he says or does. It's just that he's mostly good for America ... and the world.

More people need to watch Sicko, and while you're at it, re-watch Bowling for Columbine and Farenheit 9/11. Anyone looking for "real change" could remind themselves about what those movies were saying.

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The Selfish Genius

 
I'm still waiting for my copy of The Selfish Genius to arrive. I ordered it weeks ago when I first heard of the author, Fern Elsdon-Baker. She wrote a promotion piece in New Scdientist last month where she outlined her main thesis; namely, that epigenetics and Lamarckian evolution are challenging the Dawkins dogma. I noted that she seemed to have completely missed the adaptationist-pluralist debate—the real challenge to the Dawkins viewpoint that's been playing out over the past three decades [The Collapse of the "Dawkins Dogma"].

This is a remarkable omission for someone who claims to be a scholar of this history. I was looking forward to reading a copy of The Selfish Genius in order to see for myself just how wrong she could be. As most of you know, I'm an advocate of pluralism and "evolution by accident"—a viewpoint that's the exact opposite of Dawkins' adaptationist position. I'm not opposed to overthrowing the "Dawkins Dogma," but I don't think that epigenetics is the real threat. It's just a fad.

I won't have to post a review of The Selfish Genius because Razib Khan (of Gene Expression) has already posted a lenghty review and I doubt very much there's anything I could add. Read it at: The Selfish Genius, mind your manners Dr. Dawkins!

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The Evolution of God

 
Robert Wright is a journalist known for founding Bloggingheads.tv. He has written several books, notably The Evolution of God, which was published this year.

His schtick is the compatibility of science and religion. According to him, accommodation will be achieved once believers come to accept natural selection and convert to some form of deism, and once atheists learn to accept that this kind of wishy-washy (not his terminology) religion is compatible with science.

I recently linked to a blogging heads discussion between Wright and Daniel Dennett in which I criticized both of them for misunderstanding evolution. Wright seems to have bought into the Dennett idea of natural selection being the only mechanism of evolution. Wright also believes that natural selection will inevitably lead to sentient beings with a sense of moral purpose.

If this is true then science has to accept the fact that God could have cooked the books so that creatures would eventually evolve to the point where they were willing to worship him and offer sacrifices. And they would do so in spite of the absence of scientific evidence for the existence of such a non-interventionist, deistic, God. All the stories about an interventionist God must be wrong. If you're a deist, there was no deluge, no chosen people, and no divine Jesus.

Under such a scenario, I often wonder how believers would know what kind of God to worship. How do you distinguish between a Satan and Gitche Manitou if the deistic god has gone to such great lengths to be hands off during the evolution of sentient beings?

Robert Wright's latest foray into this debate comes as an op-ed piece in yesterday's New York Times: Direction and Purpose in Evolution. He reiterates the point that both sides of the war between science and religion are wrong. He is a confirmed accommodationist.

There are atheists who go beyond declaring personal disbelief in God and insist that any form of god-talk, any notion of higher purpose, is incompatible with a scientific worldview. And there are religious believers who insist that evolution can't fully account for the creation of human beings.

I don't want to discuss that argument except to say, for the record, that I'm one of those who insist that's there's no evidence of purpose in the evolution of life. Any talk of there being a direction to evolution, where sentient beings are the ultimate goal, founders on a massive lack of evidence in support of such a notion.

However, I'm willing to accept that biological science is more or less compatible with the existence of a supernatural being who created life on Earth and then stepped back to let history play out according to the standard rules of physics and chemistry.

Where I differ from people like Wright and Dennett is that my version of evolution is not restricted to natural selection. In my view of evolution, accident and chance play important roles at both the macro- and micro levels. Mass extinctions are just one example at the macro- level and random genetic drift is the most important example at the micro- level.

Why is this important? It's important because it gets us away from "design" talk. Most believers are committed to talk of design and purpose because otherwise life has no meaning. If they accept evolution then they make science and religion compatible by evoking God as the cause of natural selection. In this accommodationist scenario, God achieves his purpose through the law of natural selection.

Some philosophers and evolutionary biologists also believe that evolution is an algorithmic process, relying (almost) exclusively on natural selection as the driving force. Some, like Daniel Dennett, use metaphors such as building skyscrapers in order to illustrate their view of purposeful evolution. By invoking purpose and design, these philosophers and evolutionary biologists lend support to those believers who also see evidence of design and purpose. Robert Wright is correct to point out that the two groups, atheistic adaptationists and deistic believers, are not that far apart.

I bring good news! These two warring groups have more in common than they realize. And, no, it isn't just that they're both wrong. It's that they're wrong for the same reason. Oddly, an underestimation of natural selection's creative power clouds the vision not just of the intensely religious but also of the militantly atheistic.

If both groups were to truly accept that power, the landscape might look different. Believers could scale back their conception of God's role in creation, and atheists could accept that some notions of "higher purpose" are compatible with scientific materialism. And the two might learn to get along.

This is a little confusing because many of the "militant atheists" he complains about are strong adaptationists who are only too willing to explain everything by natural selection. Those scientists clearly see design and purpose in evolution, but that doesn't make them accommodationists.

Robert Wright evokes evolutionary psychology in defense of accommodationism. Using the "moral law" example, he points out that natural selection can explain morality and believers have to accept this "fact." However, those same believers can take comfort in the idea that God planned this when he created natural selection in the first place, so the evolution of a "moral law" is consistent with belief in a deistic God.

Indeed, this dynamic of reciprocal altruism, as mediated by natural selection, seems to have inclined us toward belief in some fairly abstract principles, notably the idea that good deeds should be rewarded and bad deeds should be punished. This may seem like jarring news for C. S. Lewis fans, who had hoped that God was the one who wrote moral laws into the charter of the universe, after which he directly inserted awareness of them in the human lineage.

But they may not have to stray quite as far from that scenario as they fear. Maybe they can accept this evolutionary account, and be strict Darwinians, yet hang on to notions of divinely imparted moral purpose.

The first step toward this more modern theology is for them to bite the bullet and accept that God did his work remotely — that his role in the creative process ended when he unleashed the algorithm of natural selection (whether by dropping it into the primordial ooze or writing its eventual emergence into the initial conditions of the universe or whatever).

Of course, to say that God trusted natural selection to do the creative work assumes that natural selection, once in motion, would do it; that evolution would yield a species that in essential respects — in spiritually relevant respects, you might say — was like the human species. But this claim, though inherently speculative, turns out to be scientifically plausible.

Wright is mostly directing his arguments at theists in order to convince them that they can accept evolution without abandoning the concepts of a God-given morality and a life with meaning and purpose. He spends less time trying to convince atheistic scientists because he believes that his interpretation of the science is correct. His blogging head conversation with philosopher Daniel Dennett has convinced him that most scientists think this way.

For starters, there are plenty of evolutionary biologists who believe that evolution, given long enough, was likely to create a smart, articulate species — not our species, complete with five fingers, armpits and all the rest — but some social species with roughly our level of intelligence and linguistic complexity.

And what about the chances of a species with a moral sense? Well, a moral sense seems to emerge when you take a smart, articulate species and throw in reciprocal altruism. And evolution has proved creative enough to harness the logic of reciprocal altruism again and again.

This is the part I dispute. I don't believe that the evolution of some sort of sentient species was inevitable. And I don't believe there's a universal moral law that evolved due to natural selection. My version of evolution, involving copious amounts of chance and accident, just happened to produce sentient beings on this planet. I suspect that if we looked at a thousand planets with life we wouldn't see another example.

Furthermore, I think that our sense of proper morality is mostly cultural, not genetic. We didn't "evolve" a hard-wired guilty feeling whenever we treated people unfairly. After all, people in many cultures supported slavery and mistreatment of women for thousands of years without being consumed by the expression of their "guilt" genes. Most of what passes for morality is not due to genes (alleles) for reciprocal altruism. Instead, a great deal of "morality" is an epiphenomenon that follows naturally whenever you have intelligent beings living together in a society that has learned the advantages of co-operation.

Robert Wright's mistake is assuming that adaptationism is the general consensus in biology. His accommodationist argument fails if science doesn't recognize design and purpose as the key paradigms of evolution.

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Intelligent Design Creationists and Lateral Gene Transfer

 
Some of you might recall an article in Nature Physics published a few weeks ago [Collectivist Revolution in Evolution]. In that article, Mark Buchanan, a physicist, mentioned that biologists were questioning the tree of life.

Buchanan gets so many things wrong I hardly knew where to begin. So, when I blogged about it I just mentioned one thing [Lateral Gene Transfer and the Return of Lamarckian Evolution]. I concluded with ...

This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it.

As expected, the creationists—intelligent and otherwise—were delighted with this latest challenge to evolution. I doesn't matter to them whether a physicist knows what he's talking about.

One of the "otherwises" is named Denyse O'Leary. She's happy to promote the idea that evolution¹ is being challenged. It's a special thrill for her to discover that biology is being questioned in a physics journal [The overthrow of Darwinism - in real life, forget the pop science media].

Denyse doesn't do any of the intellectual heavy lifting (surprise!). Instead she links to another Intelligent Design Creationist named David Tylor. Tylor is also mesmerized by the Nature Physics article. He blogged about it at: The collectivist challenge to Darwinism.

Here's part of what he said ...

Talk of unseating Darwinian evolution has not gone down well with some. Larry Moran quotes some of Buchanan's visionary words and declares: "This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it." However, we could do with more substance in arguments against this essay. Darwinism is inherently reductionistic and it can devise ways of framing HGT to fit into its own mental models. But what it cannot easily do is adopt the holistic perspectives that are emerging everywhere. This is why some of us find a framework of design to be compelling. Design provides a coherent context for systems biology, for biomimetics, and for many other contemporary areas of research. Furthermore, although our understanding of HGT is imperfect and in its infancy, design thinking provides a warrant for inferring the origin of genes capable of being transferred, and for understanding the roles played by HGT in populations.

Where to begin?

Horizontal gene transfer (HGT, also known as Lateral Gene Transfer) has been studied for six decades. We have an excellent understanding of the mechanisms; namely, transformation, transduction, conjugation, fusion, and endosymbiosis. There's nothing new there.

"Darwinism" and "Darwinian evolution" are products of the nineteenth century. The only people who are stuck in that century are the creationists. Modern evolutionary biologists have been at the forefront of "holistic" approaches since the recognition that populations evolve, not individuals. For most biologists, this happened in the 1940s. To put this into perspective, that's at least sixty years ago, or 1% of the entire history of Earth!

I'm actually quite happy to promote the "unseating [of] Darwinian evolution" as anyone who reads Sandwalk will attest. David Taylor and Denyse O'Leary are completely incapable of recognizing that legitimate challenges to the old-fashioned way of thinking about evolution are now part of mainstream biology. In fairness, what can we expect from people who think that a 2500 year old book written in Hebrew, Aramaic, and Greek still contains relevant information about science?

"Design" fails to provide a coherent context for anything. I've yet to see anyone explain how and when God intervened to create modern life.

Finally, in case David Tylor is actually interested in learning about the science he criticizes, here's a list of recent postings on the topic. I'd be happy to debate him whenever he feels ready. I'd be happy to do it on The ID Update: News and Commentary Updates for the ID Community but that blog doesn't allow comments. Isn't that strange?

1. The Tree of Life
2. Perspectives on the Tree of Life: Ford Doolittle
3. Perspectives on the Tree of Life: Day One
4. Perspectives on the Tree of Life: Day Two
5. Perspectrives of the Tree of Life: Day Three
6. On the Origins of Eukaryotes

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1. She calls it "Darwinism," just like all the other IDiots.

Creationists Made Him Do It!

 
A reader¹ alerted me to a letter by Patrick J. Keeling in the latest issue of Science: Creationists Made Me Do It.

He tells a story about hearing creationists speak in his high school biology class. What was the effect of this indoctrination? ...

For at least one sulky teenager in the small town of Owen Sound, Ontario, it took a creationist to make him into an evolutionary biologist.

This is one of the reasons why exposing high school students to the IDiots should be encouraged, not banned. They are their own worst enemy.

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1. Thank-you Grace.

Anne Wojcicki's Politically Correct View of Race

 
Anne Wojcicki is the co-founder of "23andMe" a company that will analyze your DNA for a fee. She was recently interviewed and the results are posted on the New York Times website [Genetics Entrepreneur Anne Wojcicki Answers Your Questions].

One of the questions asked about "race." Here's her reply.

A lot of the difficulty in talking about race has been a lack of agreement on what “race” means. In the past, the idea of pure races also included an ordering of certain races as inherently superior to others. We reject this idea absolutely. However, that doesn’t mean that there are no genetic differences between populations of different ancestral origin. A few of our features use the genome-wide data of reference populations from around the world to trace the origin of pieces of an individual’s genome. Some customers have complex patterns depending on where their ancestors originated. These reference populations aren’t “races”; they’re representative samples of peoples who have lived in a single place for a very long time and have thus accumulated different sets of genetic variants over time.

John Hawks noticed this and blogged about it: Modern genomics and race. He said exactly what I was thinking ...

That's a tricky piece of wordcraft -- they're not 'races'; "they're representative samples of peoples who have lived in a single place for a very long time and have thus accumulated different sets of genetic variants over time."

Uhh....I'm thinking that's pretty much the definition of race in a lot of textbooks...

Most species are subdivided into races (also called subspecies, or demes).

Humans are not an exception. Races exist. Pretending that they don't isn't going to solve the problems of racism. It just makes you look stupid.

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The Evolution of Man Scientifically Disproved

 
When David Schuller came to visit me a couple weeks ago he brought me a special present. It was a book he found in a bookstore. Dated 1925, the title is, The Evolution of Man Scientifically Disproved. The author is the Rev. William A. Williams formerly the president of Franklin College. I thought it might be interesting to present one of his “disproofs” of evolution.

You may think it unfair to dredge up a defense of creationism based on a 84 year old book. It’s not unfair because I’m using the same standards that the creationists use when they talk about “Nebraska Man” and the Scopes trial, not to mention Charles Darwin and Ernst Haeckel. It’s clear that 1925 is “modern science” from their perspective.

Furthermore, the arguments of Rev. Williams aren’t any worse than the ones used in 2009! The title page makes it clear that this is the best that creationists have to offer.

Designed. (1) As an up-to-date text book, and a companion to all other text books on evolution; and

(2) As an antidote to books in libraries teaching evolution, infidelity and atheism; and

(3) As an aid to all students, parents, teachers, ministers, lawyers, doctors, and all other lovers of the truth.

Rev. Willimas begins with a discussion of the population of the world.

The population of the world, based upon the Berlin Census reports of 1922, was found to be 1,804,187,000. The human race must double itself 30.75 times to make this number. This result may be approximately ascertained by the following computation:—

At the beginning of the first period of doubling there would just be two human beings; the second, 4; the 8, eight; the fourth, 16; the tenth, 1024; the twentieth, 1,048,576, the thirtieth, 1,073,741,824; and the thirty-first, 2,147,483,648. In other words, if we raise two to the thirtieth power, we have 1,073,741,824; or to the thirty-first power, 2,147,483,648. Therefore, it is evident even to the school boy, that, to have the present population of the globe, the net population must be doubled more than thirty times, and less than thirty-one times. By logarithms, we find it to be 30.75 times. After all allowances are made for natural deaths, wars, catastrophes, and losses of all kinds, if the human race would double its numbers 30.75 times, we would have the present population of the globe.

Now, according to the chronology of Hales, based on the Septuagint text, 5077 years have elapsed since the flood, and 5177 years since the ancestors of man kind numbered only two, Noah and his wife. By dividing 517 7 by 30.75, we find it requires an average of 168.3 years for the human race to double its numbers, in order to make the present population. This is a reasonable average length of time.

Moreover, it is singularly confirmed by the number of Jews, or descendants of Jacob. According to Hales, 3850 years have passed since the marriage of Jacob. By the same method of calculation as above, the Jews, who according to the Jewish yearbook for 1922, number 15,393,815, must have doubled their numbers 23.8758 times, or once every 161.251 years. The whole human race, therefore, on an average has doubled its numbers every 168.3 years; and the Jews, every 161.251 years. What a marvelous agreement! We would not expect the figures to be exactly the same no more be greatly surprised if one period were twice the other. But their correspondence singularly corroborates the age of the human race and of the Jewish people, as gleaned from the word of God by the most proficient chronologists. If the human race is 2,000,000 years old, the period of doubling would be 65,040 years, or 402 times that of the Jews, which, of course, is unthinkable

While the period of doubling may vary slightly in different ages, yet there are few things so stable and certain as general average, where large numbers and many years are considered, as in the present case. No life insurance company, acting on general average statistics, ever failed on that account. The Jews and the whole human race have lived together the same thirty-eight centuries with very little intermarriage, and are affected by similar advantages and disadvantages, making the comparison remarkably fair.

Also the 25,000,000 descendants of Abraham must have doubled their numbers every 162.275 years, during the 3,988 years since the birth of his son Ishmael. These periods of doubling which tally so closely, 168.3 years for the whole race, 161.251 for the Jews, and 162.275 years for the descendants of Abraham, cannot be a mere coincidence, but are a demonstration against the great age of man required by evolution, and in favor of the 5,177 years since Noah. None of the other various chronologies would make any material difference in these calculations. The correspondence of these figures, 168.3, 161.251 and 162.275 is so remarkable that it must bring the conviction to every serious student at the flood destroyed mankind and Noah became the head of the race.

Now the evolutionists claim that the human race is 2,000,000 years old. There is no good reason for believing that, during all these years the developing dominant species would not increase as rapidly as Jews, or the human race in historic times, especially since the restraints of civilization and marriage did not exist. But let us generously suppose that these remote ancestors, beginning with one pair, doubled their numbers in 1612.51 years, one-tenth as rapidly as the Jews, or 1240 times in 2,000,000 years. If we raise 2 to the 1240th power, the result is 18,932,139,737,991 with 360 figures following. The population of the world, therefore, would have been 18,932,139,737,991 decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, or 18,932,139,737,991 vigintillion, vigintillion, vigintillion, vigintillion, vigintillion/

Or, let us suppose that man, the dominant species originated from a single pair, only 100,000 years ago, the shortest period suggested by any evolutionists (and much too short for evolution) and that the population doubled in 1612.51 years, one-tenth the Jewish rate of net increase, a most generous estimate. The present population of the globe should be 4,660,210,253,138,204,300 or 2, 527,570,733 for every man, woman and child! In these calculations, we have made greater allowances than any self-respecting evolutionist could ask without blushing. And yet withal, it is as clear as the light of day that the ancestors of man could not possibly have lived 2,000,000 or 1,000,000 or 100,000 years ago, or even 10,000 years ago; for if the population had increased at the Jewish rate for 10,000 years, it would be more than two billion times as great as it is. that has ever been made, or ever can be made, much in excess of 5177 years, can possibly stand as the age of man. The evolutionist cannot sidestep this argument by a new guess. Q. E. D.

All these computations have been made upon the supposition that the human race sprang from one pair. If from many in the distant past, as the evolutionists assert, these bewildering figures must be enormously increased.

Yet we are gravely told that evolution is "science". It is the wildest guess ever made to support an impossible theory.

That their guesses cannot possibly be correct, is proven also by approaching the subject from another angle. If the human race is 2,000,000 years old, and must double its numbers 30.75 times to make the present population, it is plain that each period for doubling would be 65,040 years, since 2,000,000 ÷ 30.75 = 65,040. At that rate, there would be fewer than four Jews! If we suppose the race to have sprung from one pair 100,000 years ago, it would take 3252 years to double the population. At this rate, there would be five Jews!

Do we need any other demonstration that the evolution of man is an absurdity and an impossibility? If the evolutionists endeavor to show that man may have dissented from the brute, the population of the world conclusively shows that MAN CERTAINLY DID NOT DESCEND FROM THE BRUTE. If they ever succeed in showing that all species of animals may have been derived from one primordial germ, it is impossible that man so came. He was created as the Bible declares, by the Almighty Power of God.

The testimony of all the experts in the present Scopes trial in Tennessee (who escaped cross-examination) was to the effect that evolution was in harmony with some facts and therefore possibly true. The above mathematical calculations prove that the evolution of man certainly not true. They fail to make their case even if we grant their claims. These figures prove the Bible story, and scrap every guess of the great age and the brute origin of man. It will be observed at the above calculations point to the unity of the race in the days of Noah, 5177 years ago, rather than in the days of Adam 7333 years ago, according to Hale's chronology. If the race increased at the Jewish rate, not over 16,384 perished by the Flood, fewer then by many a modern catastrophe. This most merciful providence of God started the race anew with a righteous head.

Now, if there had been no flood to destroy the human race, then the descendants of Adam, in the 7333 years, would have been 16,384 times the 1,804,187,000, or 29,559,799,808,000; or computed the Jewish rate of net increase for 7333 years since Adam, the population would have been still greater, or 35,184,372,088,832. These calculations are in perfect accord with the Scripture story of the special creation of man, and the destruction of the race by a flood. Had it not been for the flood, the earth could not have sustained the descendants of Adam. Is not just a demonstration, decisive and final?

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A List of Banned Words

 
Carl Zimmer is teaching a course on science writing. Here's a picture of his classroom.

It's a tough job, but somebody has to do it.

Carl has banned certain words and phrases and he posted the list on his blog: The Index of Banned Words. We can all agree that "breakthrough" and "paradigm shift" must be on the list. What about the others? Share your opinion on The Loom.

I'd like to add "Darwinism," "cancer" (unless the article is actually about cancer), and "revolutionary."

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