Bacteria Fossils in Meteorites

When I first heard about the discovery of fossil bacteria in meteorites I immediately read the paper in the Journal of Cosmology [Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites: Implications to Life on Comets, Europa, and Enceladus]. The first thing I noticed was that this "journal" seemed to be of very low quality. A little bit of digging revealed that it was some sort of online journal that publishes just about everything.

The second thing I noticed was that the evidence of fossils in these meteorites was not convincing. It seemed like the author, Richard B. Hoover, was not being very skeptical about what he was seeing. I dismissed the paper, it was almost certainly not true.

Lot's of other people reached the same conclusion.

Ian Musgrove at The Panda's Thumb [Life from Beyond Earth on a Meteorite, or Pareidolia?] [Commentaries posted at Journal of Cosmology]

Phil Plait at Bad Astronomy [Followup thoughts on the meteorite fossils claim]

PZ Myers at Pharyngula [Did scientists discover bacteria in meteorites?]

Rosie Redfield at RRResearch [Is this claim of bacteria in a meteorite any better than the 1996 one?]

The Journal of Cosmology has now published 21 commentaries on the paper and only two of them are the least bit critical or skeptical of the results. That inspired the journal to insert this statement in the introduction to the article.

Official Statement The Journal of Cosmology,
Have the Terrorists Won?
Only a few crackpots and charlatans have denounced the Hoover study. NASA's chief scientist was charged with unprofessional conduct for lying publicly about the Journal of Cosmology and the Hoover paper. The same crackpots, self-promoters, liars, and failures, are quoted repeatedly in the media. However, where is the evidence the Hoover study is not accurate?

Few legitimate scientists have come forward to contest Hoover's findings. Why is that? Because the evidence is solid.

But why have so few scientists come forward to attest to the validity? The answer is: They are afraid. They are terrified. And for good reason.

The status quo and their "hand puppets" will stop at nothing to crush debate about important scientific issues, and this includes slander, defamation, trade libel... they will ruin you. Three hundred years ago, they would burn you for questioning orthodoxy. Has anything changed?

The scientific community must march according to the tune whistled by those who control the funding. If you don't do as you are told, if you dare to ask the wrong questions, they will destroy you.

JOC offered the scientific community a unique opportunity to debate an important paper, but for the most part they have declined.

The message is: Be afraid. Be very afraid. Or you will be destroyed.

Why is America in decline?

Maybe the terrorists have won.

Did you need convincing that this is not real science?

Now here's the tough question. Why did so many people immediately see that this paper was flawed while many others, including some journalists, were taken in? I think it's because many of us recognized this as an extraordinary claim that required extraordinary evidence. We also realized that if this was even close to being true it would be published as a front page story in Science or Nature. In addition, we have lived through many examples of exaggerated claims, including previous claims of meteorite fossils that proved to be untrue; not to mention the 3.5 billion year old fossils that weren't fossils [Did Life Arise 3.5 Billion Years Ago?].

It's a combination of skepticism and experience. Can that be taught?

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Zombie Theories

According to Greg Laden there are certain "theories of everything" that "will generally evolve into a zombie that won’t die and can’t be killed, potentially eating the brains of science geeks and graduate students for decades." The classic example is Aquatic Ape Theory but theories of bipedalism in humans are a close second. [The Aquatic Ape Theory as a Zombie Theory]

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When Did People First Start Knowing the One True God?

It's so easy to make fun of creationists and almost as easy to mock the so-called "theistic evolutionists" who have developed "sophisticated" ways of rationalizing Christianity and evolution. The accommodationists among us don't like to alienate the theistic evolutionists because their views are not in conflict with science—or so they say.

Let's take a look at the science behind theistic evolution. Here's an article from BioLogos that looks very interesting. It's written by Denis Alexander, Director of the Faraday Institute for Science and Religion at St. Edmund’s College, Cambridge and it's billed as A Response to Coyne, MacDonald, Ruse, and Wilkinson, Pt 2. Jerry Coyne brought it to my attention¹ [It feels so good when it stops].

Remember that Denis Alexander is at Cambridge University (UK) so he's presumably one of the top intellectuals in his field. He says,

First, it should, I hope, be clear by now that I don’t think there is any problem with using the language of “data” and “models” in this context, providing that we don’t start thinking that we’re using the terms as they’re generally used in everyday science. Since such terms are used, as we have seen, in a wide range of disciplines, there seems no particular reason not to use them here. If pressed, then I would say that their use in our present context is somewhat akin to the various models posited to provide evolutionary explanations for the origin of music.1 In other words, it is quite possible to generate plausible models for things which are consistent with various kinds of data and argument, including in this case a good deal of aesthetic insight, yet without any realistic hope of deciding between different models in the foreseeable future. If someone would prefer to label the Retelling Model and the Homo divinus Model, ‘informed speculations’, then I have no problem with that at all, except to say that in the end even speculation A may be more plausible than speculation B, so it comes to the same thing in the end. Carrying out thought experiments is the way that human knowledge expands.

Speaking of knowledge takes me to a second point, this one for the positivists. In many ways this particular discussion is one internal to the Christian community, a point that will become even more apparent below. Clearly models that discuss the possible ways in which humans first came to know God are not going to gain much traction in the minds of those who do not believe that God exists. So I wouldn’t blame atheists at all for thinking that even discussing such models is a bit of a waste of time. If I was trying to present arguments to atheists for belief in God, then this is certainly not where I would start! But my intention here is not to present arguments for belief in God, but instead to present some reflections for the world-wide community of around two billion Christians, who do as a matter of fact believe in God and, in their various ways, do believe that God can be known, and who, one presumes, do believe that theological knowledge counts as real knowledge.

...

Instead I start with a somewhat different set of questions when thinking about models such as the Retelling and Homo divinus models. Taking the corpus of Biblical literature as a whole, here we have a ‘grand narrative’ of creation, alienation from God due to human sin and disobedience, redemption through Christ, and a new heavens and a new earth. We have the possibility of fellowship with God through freely willed choice. Our nearest cousins, chimps and bonobos, to the best of our knowledge, do not. So the curious Christian is likely to ask at least some time during their lives, “Well, when did that possibility first begin? When did people first start knowing the one true God in such a way that they could pray, walk with God, and be responsible to God? When could they first be judged by God because they had sinned?” It is those kinds of questions that the Retelling and Homo divinus type of models are interested in addressing. Did all this happen rather slowly, as in the first model, or rather fast, as in the second? Notice that the questions raised are not to do with the origins of religion (however defined), which is another kind of discussion altogether, but with the origins of spiritual life, knowledge of God, the time when humans first became answerable to God for their actions. Notice also that the questions would still be there even if we had in our hands only the New Testament. It is not Genesis that poses the questions, though Genesis is clearly relevant, but rather the Christian theology of creation, sin and redemption. The themes of creation, sin and redemption keep replaying like a musical répétitif through the biblical symphony. The early chapters of Genesis is where the répétitif is first introduced, and so attracts our attention, but let us not forget the répétitif in the rest of the biblical texts.

Here's one of many possible charts showing our fossil ancestors.


So, what do you think, dear readers? When did our species first start knowing the "one true God"? Jerry Coyne is putting his money on Homo erectus but I'm thinking the correct answer is "not yet." It troubles me a bit that the majority of members of our species have never, ever, in their entire history believed in the Judeo-Christian God. That nasty little fact doesn't seem to trouble Denis Alexander. I guess that's because we rely on different ways of knowing. My way is scientific. David Alexander relies on "theological knowledge."

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[Photo Credit: This is a photo of one of our ancestors from One Million Years B.C. I don't know if she knew about the one true God.

1. I don't usually read the articles posted on The BioLogos Forum.

The Blue-footed Booby

The question of the week in New Scientist (Feb. 12-18, 2011) is, "The blue-footed booby is an extraordinary-looking bird. It has fairly dull plumage but strikingly coloured blue legs and feet. What could be the evolutionary benefit of such a conspicuous feature? Both sexes have blue feet so they don't seem to be for impressing potential mates."

This is bound to bring out the adaptationists. You can be almost certain that the answers will consist of various just-so stories based on the assumption that blue feet have to be an adaptation. Can you make up a good adaptationist story to explain the blue feet? It doesn't have to have any supporting evidence. Try and avoid explanations that rely on sexual selection—that's too easy.

The evolutionary relationship between the various booby species is shown below in a figure take from Friesen and Anderson (1997). The Peruvian and blue-footed boobies apparently diverged from a common ancestor about 200,000 years ago. The Blue-footed booby's range is northern Peru and the Peruvian booby lives in southern Peru. They do not form hybrids where their ranges overlap.

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[Photo Credit: Wikipedia]

Friesen, V.L. and Abderson, D.J. (1997) Phylogeny and Evolution of the Sulidae (Aves: Pelecaniformes): A Test of Alternative Modes of Speciation. Molec. Phylo. Evol. 7:252-260 [doi:10.1006/mpev.1996.0397]

A Creationist Objects

I get lots of email from theists and creationists. They remind me that the controversies over religion and evolution are complicated. Here's a recent letter that illustrates the problem. It's from a creationist who struggles to incorporate his understanding of evolution into a worldview that just can't accommodate it. The results are .... interesting.

I really don't know to respond to this letter.¹ Where does one begin when trying to correct such a profound misunderstanding of science?

I love your new definition of evolution as "a change in the frequency of alleles in a population over time." What happened to spontaneous and random mutations? Epigenetics blew that out of the water. I find it amusing every time I hear some evolutionists claim evolution is fact and the evidence is "overwhelming." Evolutionists have given up on fruitless attempts to prove the impossible and have implemented a new strategy of just claiming evolution has been proved by mountains of evidence.

Epigenetics proves adaptation and nothing else. It controls gene expression driven by environmental stress. It, nor any of the other theories of evolution provide for mechanisms to increase information in genomes. Hence evolutionists are confined to wild extrapolation of adaptation to prove macro evolution. Why hasn't it occurred in experiments? 50,000 generations of bacteria and still no macro evolution nor even proof of a simple DNA change much less added information in the genome. Guess why? You can't get there from here. Evolutionists look like idiots trying to make a plausible explanation why provisions for adaptation reside in what they call "Junk DNA" for millions of years before the organism is exposed to environmental changes that calls upon for them to survive.

The next time you consider calling someone an idiot you might consider there are some reading your posts that are not impressed by your insane unfounded conclusions. Allele frequencies are not going to hide the obvious shortcomings of evolution theory. Proving allele frequencies change proves epigenetics and adaptation and nothing else unless you are an idiot.

Don Berry

I have the sense of the common cow who knows how to eat the grass and spit out the cockle burrs.

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1. I do not publish email messages without first obtaining permission from the author.

Get a Job: in Victoria

From Faculty Position 2011.

University of Victoria
Biochemistry and Microbiology

Biochemist

The Department of Biochemistry and Microbiology leads in molecular biological research at the University of Victoria with strengths in structural biology, microbial pathogenesis, regulation of gene expression, and epigenetics.

The department is the academic home of the University of Victoria-Genome BC Proteomics Research Centre – an internationally recognized centre for proteomics research focused on structural proteomics, metabolomics, clinical proteomics, and protein imaging. The Centre also provides support for proteomics research in the areas of protein identification, quantitative proteomics, and biomarker discovery and validation.

Applications are invited for a tenure track position for a Biochemist at the rank of assistant or associate professor. The department is interested in applicants who intend to develop a hypothesis-driven research program that builds on a background of proteomics. The research program of the successful applicant is expected to complement the aims of the Proteomics Centre and the research strengths of the department. A strong commitment to teaching in the undergraduate and graduate programs of the department is required.

The deadline for application is 15 March, 2011. Applicants should provide electronic versions of a CV, a statement of research objectives, a statement on teaching objectives, and arrange for electronic letters from no more than 3 referees to be received by the application deadline.

The University of Victoria is an equity employer and encourages applications from women, persons with disabilities, visible minorities, Aboriginal Peoples, people of any sexual orientation and gender, and others who may contribute to the further diversification of the University.

All qualified candidates are encouraged to apply; however, in accordance with Canadian Immigration requirements, Canadians and permanent residents will be given priority.

Robert D. Burke, Chair
Department of Biochemistry and Microbiology
University of Victoria
VICTORIA, BC
Canada V8W 3P6
biocmicr@uvic.ca

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Astronomy and Biology

This is a remarkable picture. Depending on your personal preferences, you may be attracted to the sky in the background or the beautiful blue color along the shoreline of the lake. Are you an astronomer or a biologist, or both?

Phil took the picture and he explains it at: Gippsland Lakes.

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Hat Tip: another Phil at Bad Astronomy

Living Without Religion

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Carnival of Evolution: March 1, 2011

This month's Carnival of Evolution is hosted by Genome Engineering [Carnival of Evolution: March 1, 2011].

There's a ton of interesting links this month. Check it out!

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Problems with the Eukaryotic Tree of Life

Here's the ninth question my students have to answer. This is the end of the series since the test is tomorrow.

The positions of animals, fungi, and plants in the eukaryotic tree of life have been clear for decades. So why is there so much controversy today about how to construct a valid tree of eukaryotes? What are the main problems, according to Keeling et al. (2005), and how will those problems be overcome?

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Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676. [doi:10.1016/j.tree.2005.09.005]

What's Wrong with This Picture?

Here's my granddaughter Zoë at the Antwerp aquarium. She's learning biology from my daughter, the astrophysicist.

I need to get over to Belgium as soon as possible before it's too late.

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Extending the Modern Synthesis at the Molecular Level

Question eight for my students is designed to see if they have read and understood three papers that were assigned to them.

G. Ledyard Stebbins and Francisco Ayala wrote in 1981,

During the last decade no other issue has been more actively debated among evolutionists than the role of random drift. Molecular studies have shown that protein polymorphisms are pervasive in natural populations and that protein changes accompany the evolution of species. The neutrality theory of protein evolution proposes that evolution at the molecular level is largely due to random drift rather than being impelled by natural selection. But many evolutionists maintain that natural selection plays an essential role even at the molecular level. The “selectionist” and “neutralist” views of molecular evolution are competing hypotheses within the framework of the synthetic theory of evolution.

Why do they refer to “selectionist” and “neutralist” views “of molecular evolution”? Is there no debate over the role of random genetic drift except at the molecular level? Do you agree with Stebbins and Ayala that Neutral Theory and the role of random genetic drift are usually included in the description of the Modern Synthesis? Did Gould agree when he wrote his 1980 paper?

The quotation is from a paper published in response to Gould's famous Paleobioogy paper where he said that, "I have been reluctant to admit it—since beguiling is often forever—but if Mayr's characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy." (see Good Science Writers: Stephen Jay Gould for a description of what Gould thought of his own claim in 2002.) This paper is now available online. In the past, lots of people referred to it but never read it.

Gould responded to the Stebbins and Ayala paper in Gould (1982). The three papers illustrate the core of the debate over the Modern Synthesis and its possible extensions. I think it's fair to say that modern evolutionary theory has moved away from the hardened version of the 1960s but still not addressed some of the issues that Gould raised thirty years ago.

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[Photo Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]

Gould, S.J. (1980) Is a New and General Theory of Evolution Emerging? Paleobiology 6:119-130. [PDF]

Gould, S.J. (1982) Darwinism and the Expansion of Evolutionary Theory. Science 216:380-387. [PDF]

Stebbins, G.L. and Ayala, F.J. (1981) Is a new evolutionary synthesis necessary? Science, 213: 967-971. [PDF]

Extending the Modern Synthesis

Question seven for my students is very difficult. I gave it to them as a possibility for next Tuesday's exam but I've almost decided not to us it. How many of you, dear readers, could come up with a good answer?

Which of the current proposed “extensions” of the Modern Synthesis come from studies of molecular evolution? Which one of them would you definitely include if you were proposing Evolutionary Theory (version 2011)?

Think in terms of what has to be in the textbooks ten years from now when they are discussing fundamentals of evolutionary theory.

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Debating the Existence of Junk DNA

The sixth question for my students is ...

Do you think that most of the DNA in our genome is junk? Explain your answer.

This requires that the students take a position and defend it. That means they have to understand both sides of the argument in order to engage in truly critical thinking. It doesn't matter which side you take—I'll even accept a wait-and-see position if it's well argued.

We've seen repeatedly in the scientific literature and on the blogs that many professional scientists couldn't pass this question on an exam. Is it naive to think that undergraduates can master a topic like this?

[Dog Ass Plots] [Genome Size, Complexity, and the C-Value Paradox]

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Accelerated Human Evolution: Models and Data

I've prepared a bunch of exam questions for students in my molecular evolution course. I gave them out two weeks before the exam and I promised them that I would post some of these questions on my blog to see how you would answer them. I'm hoping that you, dear readers, will show my students that there really is some controversy.

Here's the fifth question.

In their 2007 paper Hawks et al. conclude,

The rate of adaptive evolution in human populations has indeed accelerated within the past 80,000 years. The results above demonstrate the extent of acceleration: the recent rate must be one or two orders of magnitude higher that the long-term rate to explain the genomewide pattern.

If the actual results demonstrate that human evolution has accelerated then why are there still scientists who dispute the conclusion?

The point of the question is the conflict between how scientists deal with data that conflicts with their model. In this case, it's scientists (like me) who are uncomfortable with the conclusions of Hawks et al. (2007). If the data they published is valid then this should be a situation where all scientists abandon their former models it light of a "nasty little fact."

But that never happens. Why?

I'd also like to discuss another topic. How many people who read the Hawks et al. paper are actually capable of evaluating the data to see if it supports the conclusions? Are we in a new age of biology where the complexity of the databases and the sophistication of the computer algorithms make it impossible for the average scientist to judge the quality of the experiments? How about reviewers, can they evaluate the methods and results?


Note: The issues get bound up with the adaptationist/pluralist debate because two of the authors on the paper published a book to promote their views. You can read some examples of the adaptationist views of Cochran and Harpending at: Examples of Accelerated Human Evolution. I don't think John Hawks supports such an adaptationist position but I'm hoping he will chime and tell us. (John is a really smart guy—on more than one occasion he has demonstrated that my arguments are full of holes. It's embarrassing.)

Another Note: Here are some blogs that you might enjoy reading if this question interests you.

Signals of recent positive selection in a worldwide sample of human populations…maybe

Signals of Positive Selection in Humans?

Overstating the obvious

SEED Reviews The 10,000 Year Explosion

Did biologists really think that human evolution stopped?

Are Humans Still Evolving?

John Hawks doesn't like random genetic drift

Genetic differences between human populations: more drift than selection?

Is Evolution Linked to Environmental Change?

Accelerated Human Evolution

Human evolution has accelerated

Are humans evolving faster?

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Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758. Epub 2007 [PubMed] [DOI:10.1073/pnas.0707650104]

Hofer, T., Ray, N., Wegmann, D., and Excoffier, L. (2009) Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection Annals of Human Genetics 73:95-108 [doi: 10.1111/j.1469-1809.2008.00489.x]

Pickrell, J.K., Coop, G., Novembre, J., Kudaravalli, S., Li, J.Z., Absher, D., Srinivasan, B.S., Barsh, G.S., Myers, R.M., Feldman, M.W., and Pritchard, J.K. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research 23 published in advance March 23, 2009 [DOI: 10.1101/gr.087577.108]