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A Test Case for CSI?

NOTE: This is a post about probability estimation, rather than about inferring design. All systems – whether designed or not – have a certain level of specified complexity associated with them. Only if that level exceeds a certain threshold can we reliably infer intelligent design. The definition of a pattern’s specified complexity makes reference to P(T|H), the probability of a pattern T with respect to the chance hypothesis H. In this case, the pattern we see is an observed structure in a meteorite, and there are two competing hypotheses as to how it arose (leaving aside the possibility of contamination). What I’m interested in is how we would calculate the probability of that pattern if it arose abiotically, as opposed to the probability of that pattern if it is a bacterial fossil. It’s this kind of number-crunching which I feel we need to become proficient at. It would definitely be a feather in our caps if the ID movement could develop a readily utilizable metric to assist NASA in evaluating claimed discoveries of life from outer space. – VJT.

Recently, NASA scientist Richard Hoover looked at some slices of three very rare meteorites using an electron microscope technique called Field Emission Scanning Electron Microscopy, and saw what he believes to be tiny fossils of Cyanobacteria. Hoover’s article, Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites has generated a storm of controversy. Physicist Rob Sheldon has recently blogged about Hoover’s findings here and responded to some common criticisms of Hoover’s work here. Alan Boyle’s report on MSNBC is available online here. Science blogger Dan Satterfield has a post about Hoover’s discoveries here, and a review by “Discover” magazine correspondent Phil Plait can be found here. A critical review by microbiologist Rosie Redfield can be found here, while P.Z. Myers’ dismissal of Hoover’s claims is available online here.

I thought this would be an interesting test case for the concept of complex specified information (CSI), which has been getting quite a bit of attention on this blog recently (see for instance Mathgrrl’s post here, and my posts here and here). So without further ado, let’s proceed.

What is Hoover claiming?

Hoover describes his findings as follows:

A number of biominerals and organic chemicals (that are interpreted as biomarkers when found in Earth rocks) have been detected in CI1 carbonaceous meteorites. These include weak biomarkers such as carbonate globules, magnetites, PAH’s, racemic amino acids, sugar alcohols, and short chain alkanes, alkenes and aliphatic and aromatic hydrocarbons that are produced in nature by biological processes but can also be fomed by catalyzed chemical reactions such as Miller-Urey and Fisher-Tropsch synthesis. However, the CI1 meteorites also contain a host of strong biomarkers for which there are no known abiotic production mechanisms. These include magnetites in unusual configurations (framboids and linear chains of magnetosomes), protein amino acids with significant enantiomeric excess, nucleobases (purines and pyrimidines), and diagenetic breakdown products of photosynthetic pigments such as chlorophyll (pristine, phytane, and porphyrins), complex kerogen-like insoluble organic matter and morphological biomarkers with size, size range and recognizable features diagnostic of known orders of Cyanobacteriaceae and other prokaryotic microfossils. (Emphasis mine – VJT.)

At the end of his article, Hoover summarizes his argument for identifying the structures he observed in carbonaceous meteorites as fossilized bacteria from outer space:

It is concluded that the complex filaments found embedded in the CI1 carbonaceous meteorites represent the remains of indigenous microfossils of cyanobacteria and other prokaryotes associated with modern and fossil prokaryotic mats. Many of the Ivuna and Orgueil filaments are isodiametric and others tapered, polarized and exhibit clearly differentiated apical and basal cells. These filaments were found in freshly fractured stones and are observed to be attached to the meteorite rock matrix in the manner of terrestrial assemblages of aquatic benthic, epipelic, and epilithic cyanobacterial communities comprised of species that grow on or in mud or clay sediments. Filamentous cyanobacteria similar in size and detailed morphology with basal heterocysts are well known in benthic cyanobacterial mats, where they attach the filament to the sediment at the interface between the liquid water and the substratum. The size, size range and complex morphological features and characteristics exhibited by these filaments render them recognizable as representatives of the filamentous Cyanobacteriaceae and associated trichomic prokaryotes commonly encountered in cyanobacterial mats. Therefore, the well-preserved mineralized trichomic filaments with carbonaceous sheaths found embedded in freshly fractured interior surfaces of the Alais, Ivuna, and Orgueil CI1 carbonaceous meteorites are interpreted as the fossilized remains of prokaryotic microorganisms that grew in liquid regimes on the parent body of the meteorites before they entered the Earth’s atmosphere. (Emphasis mine – VJT.)

Relevance for CSI

Uncommon Descent readers will recall that Professor William Dembski defines the specified complexity Chi of a pattern T given chance hypothesis H, minus the tilde and context sensitivity, as:

Chi=-log2[10^120.Phi_s(T).P(T|H)]

where Phi_s(T) is the number of patterns for which S’s semiotic description of them is at least as simple as S’s semiotic description of T
and P(T|H) is the probability of a pattern T with respect to the chance hypothesis H.

However, if Hoover were right about absence of known abiotic production mechanisms for the strong biomarkers he observed, that would create major problems for the calculation of P(T|H), and hence CSI of the structures he observed.

Are the structures really bacteria?

But is Hoover right in claiming that abiotic processes cannot account for the structures he observed in meteorites? Microbiologist Rosie Redfield begs to disagree:

He spends a lot of text discussing the morpohlogical similarities of these filaments to cyanobacteria, but I don’t regard these similarities as worth anything. Filamentous bacteria are very morphologically diverse, and additional variations in appearance are likely to result from inconsistent preparation for electron microscopy. It’s probably pretty easy to find a bacterial image that resembles any fibrous structure. In the absence of any statistical evidence to the contrary, it’s prudent to assume that such similarities are purely coincidental.

Rocco Mancinelli, senior research scientist at Bay Area Environmental Research Institute was also skeptical:

As a microbiologist who has looked at thousands of microbes through a microscope, and done some of my own electron microscopy, I see no convincing evidence that these particles are of biological origin.

“Disover” magazine’s Phil Plait was also underwhelmed, writing that Hoover “is basing a lot of this on the shape of the structures he sees… but looking like a microbe doesn’t make them a microbe!”

P.Z. Myers was even more dismissive in his scathing review of the findings:

The extraterrestrial ‘bacteria’ all look like random mineral squiggles and bumps on a field full of random squiggles and bumps, and apparently, the authors thought some particular squiggle looked sort of like some photo of a bug. This isn’t science, it’s pareidolia…

I’d be more impressed if they’d surveyed the population of weird little lumps in their rocks and found the kind of consistent morphology in a subset that you’d find in a population of bacteria. Instead, it’s a wild collection of one-offs.

If these critics are correct, then the factor P(T|H) which appears in Professor Dembski’s equation for calculating complex specified information (CSI) is actually quite high.

But are they right? Physicist Rob Sheldon contends that some experts in bacteriology concur with Hoover’s claims that the structures he observed are specific to certain species of bacteria:

But even if, like Rosie, you claim that lots of abiotic stuff looks biological, then you had better explain why numerous European academicians who are experts in algae and bacteria have examined Hoover’s photographs and agree with him that these are not just identifiably biological, but identifiable by genus and species.

I look forward to hearing more from Rob Sheldon about the verdicts of these European experts, and if Rob could forward any articles by these experts to me, I’d be immensely grateful.

What about contamination?

The other major concern, of course, is contamination. The risks of it occurring in a study like this are very real, as microbiologist Rosie Redfield points out:

An important concern with this kind of study is contamination with terrestrial organisms before examination. He doesn’t say how the meteorites have been stored before he obtained them, nor how the surfaces of the meteorites were treated before being fractured and examined. He doesn’t say how they were fractured – might they have been cut with a scalpel blade or just pressed on until they crumbled? He says that the tools were flame-sterilized, but not what the tools were or how they were used.

She concludes: “As evidence for life this is pathetic.”

“Disover” magazine’s Phil Plait concurs, writing that “the major problem here is contamination.”

Rocco Mancinelli, senior research scientist at Bay Area Environmental Research Institute, was also very concerned about the possibility of contamination:

The techniques used may not have been appropriate for these types of analyses. It is stated that the implements were flame-sterilized, with no details of how this was performed. Were the implements placed in the flame of a Bunsen burner? If so, sometimes soot can get on them at the microscopic level. The usual procedure for flame sterilization is to dip the implements in ethanol then burn the ethanol off. Yet, these would be inappropriate for this type of analysis. You need to have everything clean and then bake at 550 degrees C overnight. These missing details would cause me to question not just about the photos, but the elemental analyses as well. I am also disturbed about the lack of nitrogen. There should be more. There are many technical flaws in this paper.

However, physicist Rob Sheldon counters that contamination is an enormously unparsimonious hypothesis in this case:

Wouldn’t recent contamination be a much more conservative explanation of these biofossils?

Well it would if we could explain (a) how to make microfossils in the first place; (b) how to make them in, oh, the 12 hours it took to collect the meteorites and put them in storage; (c) how to eliminate 12 of the 20 essential amino acids from the meteorite; (d) how to reduce the nitrogen content of the fossils to below 0.5% when 15,000 year-old mammoth hair shows no loss of nitrogen; (e) how to make fossils from organisms last seen on Earth 400 million years ago; (f) how to make the fossils out of isotopically meteoritic material not found on Earth; (g) how to make fossils out of super soluble salts and then combine them with the meteoritic material in such a way as to make them appear intrinsic; (h) how to make fossils with 10nm “fibrils” exquisitely preserved; (i) how to make recent contamination fossils inside a well-formed “fusion crust” of sterile melted meteoritic material; etc. Well, you should just read the paper rather than my summary. My point is that we don’t know how to do any of these things, so that a “contamination hypothesis” actually raises more questions than it answers. The simplest answer is that these really are indigenous microfossils from ancient extraterrestrial microorganisms.

Summary

As I see it, there are two rival hypotheses we should consider here: terrestrial contamination, and the possibility that the structures observed are not bacteria anyway. I think we should investigate the latter hypothesis first. We need to know if the structures really are bacteria before we worry about where they came from.

I’d now like to invite comments from readers with specific suggestions as to how P(T|H) might be calculated for the chance hypothesis that the structures observed by Hoover are non-biological. Here are my own ideas. As a first step, we need to count the number of points of similarity between the structures Hoover photographed and the species of bacteria which most closely resemble them. Second, we need to rank each of these points of similarity in decreasing order of likelihood, with respect to the chance hypothesis that their similarity to bacteria is entirely coincidental. Third, we need to quantify the probabilities that each of these features arose by chance, and finally we need to calculate an overall figure which represents the likelihood that the structures observed, taken as an ensemble, arose by chance in each meteorite.

Any takers?

P.S. If readers have any further comments made on the measurement of CSI, CSI-lite or kairosfocus’ X-metric, they are welcome to make them here as well.

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5 Responses to A Test Case for CSI?

  1. VJT:

    I am slightly puzzled.

    I can easily enough see how the per aspect explanatory filter [a broad view of the sci method] — which is obviously broader than the design fork of the filter, is applicable.

    But this is not a specifically design detection problem. Unless, you mean to suggest fraud? Or, maybe accident?

    What we have are some reported meteoritic rocks with some structures that look a lot like certain unicellular organisms.

    Is this a natural regularity, in the form of crystallisation or deposition of some sort? A fossil life form? Contamination on top of the life form?

    Crystallisation and deposition would be dominated by regularities and possibly chance. Filament forming minerals can come in bent shapes, even S-shapes.

    Organics may come in by accidental contamination [i.e. chance], but of course the pattern of particular molecules, if accurately observed, may be interesting.

    Both these would — “naturally” — seem to be dominant explanations, certainly over either fossilisation or fraud. And certainly we do not wish to err on the side of the last two.

    I doubt that fraud is even seriously on the table. Let’s leave this one out of reckoning.

    Fossilisation a la earth impact and so into space then back is a possible route, or even wafting to Mars and back again.

    But we need to rule out the possibilities that on the principle of it is better to make a conservative error, should prevail.

    So, the candidate to beat is

    H0: crystallisation, deposition and/or contamination.

    After that,

    H1: lofted earth rocks with fossils that have returned.

    Beyond that,

    H2: fossils making a round trip to Mars and back again. (Hugh Ross has long argued for a very long time for seeding of Mars with earth microscopic life, in the natural course of things.)

    H3: Novel, extraterrestrial life that is coincidentally almost just like ours is a bit strained just now (though on design and panspermia or the like, it is possible).

    But, we keep our options open.

    So, here are some chance and necessity scenarios, in order of “conservative” thinking.

    Others may want to adjust or elaborate, then evaluate on evidence.

    GEM of TKI

  2. Sorry on a rather messed up post.

  3. Hi kairosfocus,

    Thanks foir your comments. Just to be clear: this is a math post rather than a design-inference post. I’ve added a comment at the beginning explaining why we need to be good at math, when calculating CSI.

    In this case, for the abiotic hypothesis, I think P(T|H) should be easy to estimate, in principle. All we need is sufficient information about the frequency of structures having various shapes in rocks. That’s a data collection problem. If we break up the shapes into small enough parts, we can calculate the probabilities for complex shapes, so it should be easy to calculate P(T|H), I think.

  4. Thanks foir your comments. Just to be clear: this is a math post rather than a design-inference post. I’ve added a comment at the beginning explaining why we need to be good at math, when calculating CSI.

    Can this be broken up into three (or more) separate functions?

    1. calculate_complexity

    2. calculate_specificity

    3. calculate_information_content

    For ID, if it doesn’t. meet the complexity criterion, would it even go any further?

    2. calculate_specificity if (calculate_complexity greater_than MIN_COMPLEXITY_REQUIRED)

  5. VJ,
    Your suggestions are well-taken, and I encourage you to peruse the archives of the SPIE “Instruments and Methods for Astrobiology” conference which is holding its 14th annual conference this coming Aug 22-25 in San Diego.
    By looking over the talks, you will discover:

    a) Russian Academicians (no directly comparable office in America, perhaps Nobel-prize winner comes close) Galimov and Rosanov have written papers on biomarkers and fossil identification. Over the years, several French, Belgian, and German scientists of some stature have written supporting papers. While one cannot go by reputation alone, all these scientists are a rank or two above PZ Myers, Rosie Redfield and Rocco Mancinelli. Phil, of course, isn’t even competing as a scientist. BTW, Rocco was the editor at IJA, and his obvious bias was the reason Hoover sent his paper to JOC instead. It is revealing that Rocco’s rage is related to the fact Hoover got his paper published at all. With those kind of editors, who needs enemies?

    b) Perusal of the 13 abstract books will reveal that Hoover always invites his skeptics to the meetings to present their best case. Somewhere around the 9th or 10th meeting which I attended, we had a skeptic claiming that many abiotic artifacts can be confused with biology. His best pictures were a joke, resembling shavings on the floor of a machine shop, but nothing even vaguely biological. In contrast, a scientist who devises metrics for computer assisted photo-identification (think, finding camouflaged tanks from UAV photos) showed how biology has enormous anti-entropic (ie. Shannon information) indices that stand out from abiotic artifacts. Your test case not only has been tested, but is busy making money for entrepreneurs.

    c) Abiotic synthesis of chloryphyll or even nucleobases has foiled the best attempts of Nobel prize-winning chemists for 40 years. This is not to say that somebody didn’t just synthesize RNA abiotically in the lab this year, but remember how many years it has been since urea was first abiotically synthesized. Now, putting that chemistry lab into a randomly directed warm pond and still getting chlorophyll out is right up there with Hoyle’s tornado in a junkyard constructing a 747. When Hoover says all of these biomarkers require life, he is not only understating, but the mathematics of physical chemistry are both iron-clad and on his side. P(T|H) is both calculable and precisely what Hoover says it is. There is no mystery.

    d) Contamination has been the agreed-upon attack ever since Anders’ wife had a tryst with Nagy. But Anders had to build an elaborate fake to win the debate. The current crop of disbelievers merely invoke the magic incantation. As Hoover’s paper shows, contamination fails to explain any of his data. This somehow doesn’t convince the skeptics, who evidently are also unable to calculate P(T|H) for biomarkers as well. However I take solace in what an Anglican priest once said to me–”I have all the right enemies.” Go look at Rosie’s bio & picture and compare to Hoover’s. For that matter, read a blog of PZ Myer and then compare to Hoover’s paper. Read the editorials in Discover magazine along with Phil Plaitt’s reviews, and then reread Hoover. Very quickly you will find that Hoover has all the right enemies.

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