More on the world’s earliest fossils: they’re real!

August 28, 2011 • 8:25 am

A few days ago I posted on the discovery of the world’s earliest known fossils—sulfur-metabolizing bacteria from a site in western Australia, with the bacterial “microfossils” dated at 3.4 billion years old. (Earth is 4.54 billion years old, which means that life originated no later than 1 billion years after Earth’s formation).  The paper, whose reference and link is below, was by Dave Wacey et al., with Martin Brasier as the last (i.e., “senior”) author.

I was a bit concerned, then, when I saw P. Z. Myers had a few concerns about this paper at Pharyngula, concerns that “gave him pause.”

P.Z.’s first worry was that the fossil cells seemed too large to be prokaryotes. The paper of Wacey et al. shows, as P. Z. said:

. . . lots of cells with 10-30µm diameters. And the authors come right out and report that:

‘The size range is also typical of such assemblages, with small spheres and ellipsoids 5-25 µm in diameter, rare examples (<10) of larger cellular envelopes up to 80 µm in diameter, and tubes 7-20 µm across (see ref. 24).”

How odd. When I poke into the nervous system of an embryonic insect or fish, those are the sizes of cells I often see (well, except there aren’t many tubes of that size!). When I poke into a culture or embryo contaminated with bacteria, they’re much, much smaller. So maybe paleoarchaean bacteria tended to be larger?”

P. Z.’s second concern was that “reference 24” cited by Wacey et al. in support of the size ranges of fossil bacterial assemblages was in fact a paper by J. William Schopf. This disturbed Myers because Schopf’s earlier claim to have found the oldest microfossils on earth (3.465 billion years old) has since been discredited; as P.Z. said, Schopf’s microfossils form “a data set that’s widely considered artifactual now.” And Schopf’s largest cells were from his oldest samples, with cells getting smaller as the samples came from successively younger strata.

These considerations gave the estimable Dr. Myers some reservations about Wacey et al.’s conclusions, and at the end of his report  he asks “…isn’t this just a little bit strange? Maybe there are some micro people out there who can reassure me that this isn’t a surprising result.”

I was a bit distressed about this since I hadn’t noticed those “problems.”  I then checked them out since I don’t want to report stuff that’s wrong or dicey.  So I contacted Dave Wacey and Martin Brasier about P. Z.’s reservations.  And I’m happy to report that there’s no problem with the Wacey et al. paper.  What appears below is a bit technical, and I’m posting it to put the record straight, but if you’re following the early-fossil literature, you should read it.

Here’s what Martin Brasier wrote me, which I post with his permission:

1) Re the large size of the bacterial fossils shown:

The first point is that the larger microfossils proved to be the easiest to image and showed more convincing cellular features, so that there is a bias towards the illustration of large forms in our Figures 1 and 2. In fact, the majority of the microfossils from the Strelley Pool arenite actually fit into the same sort of size distribution patterns as seen in the younger Gunflint and Bitter Springs cherts. This is clearly shown within our Supplementary Figure 6.

Regarding the suggestion that bacterial cells tend to be small, this approach no longer looks safe. Sulphur bacteria have members that are particularly large today (12 to 160 μm). They reach great size because of cell vacuoles within them (e.g., AHMAD, A.,  BARRY, J.P. and NELSON, D.C. 1999. Phylogenetic Affinity of a Wide, Vacuolate, Nitrate-Accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Appl. Environ Microbiol. 65, 270-277). Hence unsheathed Beggiatoa filaments can often reach a width of 65 to 85 μm (range about 20-140 μm). Individual cells can reach 20 by 70 μm. Multiple Thioploca filaments (2-43 μm) usually occupy a single sheath (the part that preserves). Coccoid Thiomargarita namibiensis can be 100–300 µm wide, but can sometimes reach 750 µm.

It would be unwise to speculate about the possibilities of a larger cell size in early bacteria. But we note that microfossils reported from the 3.2 Ga Moodies Group of South Africa can be almost ten times the diameter of those found in the Strelley Pool rocks. See JAVAUX, E., MARSHALL, C.P. and BEKKER, A. (2010). Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits. Nature 463, 934-939.

2) Re the concerns of PZ Myers about use of a Bill Schopf reference

Reference 24 in our paper is NOT the Schopf (1993) article about the Apex microfossils – it is Schopf’s 2006 Phil Trans R Soc paper that was a summary of ALL microfossil claims from units older than 2.5 Ga known at that time. There were actually 40 occurrences of Archaean microfossils described by Schopf in this paper. From younger rocks, he describes 10-28 µm tubular sheaths from the Ghaap Dolomite and 16-23 micron coccoids from the Sheba Formation. (See his Table 2.) Those records are what we were referencing.

It is true that our views on some of these records has been, and remains, cautious. See, for example,  BRASIER, M.D., McLOUGHLIN, N., GREEN, O., WACEY, D. 2006. A fresh look at the fossil evidence for early Archaean cellular life. In Cavalier-Smith, T., Brasier, M.D. & Embley, T..M. (Eds) Major Steps in Cell Evolution: Palaeontological, Molecular and Cellular evidence of their timing and global effects.Philosophical Transactions of the Royal Society, Series B, volume 361, 887-902. See also the book by David ­Wacey (200) “Early Life on Earth. A Practical Guide”. Springer, Dordrecht.

For those who are interested, our re-interpretation of the 3.46 Ga Apex microfossils has been set out afresh in a new monograph: BRASIER, M.D., GREEN, O.R., LINDSAY, J. McLOUGHLIN, N., STOAKES, C., BRASIER, A. & WACEY, D. 2011. Earth’s Oldest Putative Fossil Assemblage from the 3.5 Ga Apex Chert, Chinaman Creek, Western Australia: A Field and Petrographic Guide. Records of the Geological Survey of Western Australia, Perth. This is now available on the GSWA website and on the Academia website. Out views on those follows has not changed from that we set out in 2002. We saw no need to cite the latter paper as its arguments are widely known.

Caturday felids: cat ladders

August 27, 2011 • 8:25 am

There are all kinds of specialized cat websites: cats that look like Hitler, cats with naked people, cats that jump into boxes, but this one is up there with the weirdest. It’s Cat Ladders, showing all the weird and wonderful devices people have constructed to allow their kittehs free access to upper-floor apartments.  I’ve never seen one of these things, but apparently they’re not uncommon in Europe. Here are a few, but the site has many more: the author claims that “right now the website contains approximately 967 different ladders from 32 countrys” [sic].

From Switzerland, showing the characteristic Swiss tidiness:

London:

The Netherlands:

Germany:

And Switzerland again:

Finally, a video of one in use:

If you have a cat ladder, either inside or out, email me a photo.

(anti-)Adam and Eve video

August 26, 2011 • 10:40 am

Over at YouTube, “ProMTH” has made a very nice 17-minute video summarizing the Adam and Eve controversy—that is, all the reasons why belief in a literal Adam and Eve, an idea absolutely refuted by modern genetics, is essential for a coherent Christian theology.  There’s a lot of stuff here that I haven’t mentioned in our discussions of this issue, especially material from scripture, so if you want a full take on the issue, you can’t do better than watching this:

h/t: Luke

An atheist who almost believes in God

August 26, 2011 • 10:39 am

Well, it’s really hard to tell about Dori Hartley from her PuffHo piece, “The soulful atheist.”  I’d like to say that she’s a kindler, gentler atheist (she certainly believes she is), but she might as well be religious, because she seems quite susceptible to Chopra-ian woo.  Hartley, an author and illustrator, professes this up front:

Now, I’m not one of the militant atheist-supremacists. In fact, I refer to myself as an atheist simply to clarify that I do not believe in a deity. Outside of that, I’m not married to the title nor do I use it to define myself. It’s one of those “for lack of a better word” words.

Militant? Atheist-supremacist? (That’s a new one on me!) Clearly she wants to distinguish herself from those odiferous god-deniers like Dawkins and Hitchens. And she says this:

And as an “atheist,” I can tell you this:

I pray.
I have faith.
I believe in the cosmic consciousness.
I live in gratitude.
I am moved to tears by the beauty that is nature.
I feel the intensity of great love.

Well, she’s not praying to God, but to the “cosmic mass mind”, whatever the hell that is.  And her “faith” is this:

I believe in the invisible and the intangible. I have absolute faith in the universe, in nature and in the balance of energy. My faith is unshakeable. I just don’t have faith in the same power “name” as you.

Now what kind of faith does she have in the universe, nature and “the balance of energy”? If it’s just that the universe obeys certain physical laws, that tigers eat antelopes, and that the second law of thermodynamics holds, well, that’s not really faith, but confidence in the findings of science. She uses the label of “faith” to conflate this with religion. After all, she’s not one of those militant atheist-supremicists.

She never defines “cosmic consciousness,” except to say that it’s “the concept of endless energy, all being projected and retracted on a nonstop basis, forever and ever, inwards and outwards, in every angle, etc, etc.”  Salacious metaphors aside, this is just nonsense.

The ending is really something:

So, yes, atheists can feel love, gratitude, faith, even spirituality. Like I’ve said, I’m not one of the militant types who needs to put anyone else down for their beliefs. I’m truly into the “live and let live” idea. While I do love science, I’m not here to shove Darwin or Hawking down anyone’s throat. In fact, if God is what you believe in, I’m all for it if it makes you happy, because that’s all we can ask for in this life: A little bit of happiness.

Nope, she’s not an atheist supremacist: she simply thinks that she’s better than all those other nasty atheists.

And of course she’s completely oblivious to all those other problems of religion. If it “makes you happy” to throw acid in the faces of schoolgirls, or torture little children with thoughts of hell, or let a mother and baby die rather than abort the baby, or let girls get cervical cancer rather than let them get vaccinated for HPV and have safer sex, well, those things are okay.  After all, God is love.

How many species are there on Earth?

August 25, 2011 • 5:56 am

The short answer:  about 9 million, not counting bacteria. That’s according to a new paper in PLoS Biology by Camilo Mora et al. (see also the perspective by Robert May in the same issue; both paper and perspective are free, and you should definitely read Bob’s one-page piece).

The issue of how many species inhabit our planet is a hot one: I’m often asked about it by journalists or in lectures, despite the fact that I have virtually no expertise in this area.  We know that about 1.2 million species have been described, but we also know that that’s a gross underestimate of the true number. Any time somebody samples the insects in the rain forest, for example, a large number of new species turn up, and only Ceiling Cat knows how many species of nematodes and other worms live underground.  And then there’s the real can of worms: the bacteria and archaea (see below). My usual answer to the question of “how many species?” is “probably between 5 and 50 million species.”  Well, at least I was in the right range.

Here’s the authors’ conclusion, breaking down the number of species by group; I’ll then briefly describe how they calculated these numbers (my emphasis):

When applied to all eukaryote kingdoms, our approach predicted ~7.77 million species of animals, ~298,000 species of plants, ~611,000 species of fungi, ~36,400 species of protozoa, and ~27,500 species of chromists; in total the approach predicted that ~8.74 million species of eukaryotes exist on Earth (Table 2). Restricting this approach to marine taxa resulted in a prediction of 2.21 million eukaryote species in the world’s oceans.

This means that about 1.2/8.7, or roughly 14%, of all Earth’s species have been described. Note as well that about 89% of Earth’s species (7.77/8.74) are animals, and that the vast majority of those animals are insects (see second graph below).  It was in fact Bob May who said, “To a first approximation, all animals are insects.”

How did they figure this out?  By using a two-step process.  First , they looked at “higher” taxa—phyla, classes, orders, family, and genera—and examined how the number of described taxa has increased over time, as well as the number of species. As you see from the graph below, which examines only animals (“Animalia”), every level above that of species is reaching an asymptote, while the number of species themselves continues to increase non-asymptotically.


Figure 1 from Mora et al.  The caption: “Predicting the global number of species in Animalia from their higher taxonomy. (A–F) The temporal accumulation of taxa (black lines) and the frequency of the multimodel fits to all starting years selected (graded colors). The horizontal dashed lines indicate the consensus asymptotic number of taxa, and the horizontal grey area its consensus standard error. (G) Relationship between the consensus asymptotic number of higher taxa and the numerical hierarchy of each taxonomic rank. Black circles represent the consensus asymptotes, green circles the catalogued number of taxa, and the box at the species level indicates the 95% confidence interval around the predicted number of species (see Materials and Methods).”

The conclusion from these observations is that we’re starting to approach a complete knowledge (the asymptote) of the numbers and nature of “higher” taxa, but haven’t yet approached a full knowledge of the number of individual species in these groups.

The authors then made a clever hypothesis: perhaps there is a quantitative relationship between the number of higher taxa (whose final numbers we’re starting to approach), and the number of species contained within these higher taxa.  If that were the case, we could use the asymptotic estimates for, say, number of families or orders, to estimate the final number of species they contain.

In fact, the authors did find such a quantitative relationship (see subfigure 1G above for a plot showing this): there appears to be a linear relationship on a log scale between taxonomic rank and number of asymptotic taxa.  From this you can extrapolate to the taxon of interest on the graph—species—and get an estimate of the number of species on Earth, in this case for animals.  But of course you can do this for other groups, too.

But is such extrapolation warranted? You can see whether it is by predicting from graph 1G above the number of species in well-studied groups (that is, groups, like birds and reptiles, in which we think we’ve already identified most of the species on Earth), and then comparing that prediction with the actual number of described species.  The graph below shows that for groups that have been pretty exhaustively surveyed for species, the prediction holds pretty well: the predicted number using the higher-taxon extrapolation is pretty close to the actual number of known species:

Knowing that one can pretty accurately predict the number of species on Earth by extrapolating from the number of known higher taxa, the authors got their figures above simply by doing this kind of extrapolation in less well known groups, assuming that the same relationship holds for them.  As I said, this is a clever idea, and it’s even endorsed by the critical Robert May in his accompanying perspective, “Why worry about how many species and their loss?

Jonathan Eisen, a professor at the University of California at Davis, likes the paper as well, but criticizes part of it on his website, The Tree of Life, arguing (correctly, I think) that estimates for numbers of bacteria and archaea are way off because the “higher taxon” approach is invalid for those groups.  If the estimates for these microbes really does run into the “hundreds of millions,” as Eisen thinks, then that would hugely inflate the number of species on Earth:

So all seems hunky dory and pretty interesting.  That is, until we get to the bacteria and archaea.  For example, check out Table 2. . . Their approach leads to an estimate of 455 ± 160 Archaea on Earth and 1 in the ocean.  Yes, one in the ocean.  Amazing.  Completely silly too.  Bacteria are a little better.  An estimate of 9,680 ± 3,470 on Earth and 1,,320 ±436 in the oceans.  Still completely silly. . . Their estimates of ~ 10,000 or so bacteria and archaea on the planet are so completely out of touch in my opinion that this calls into question the validity of their method for bacteria and archaea at all. Now you may ask – why do I think this is out of touch. Well because reasonable estimates are more on the order or millions or hundreds of millions, not tens of thousands.

So long will it take to catalog the rest of Earth’s biodiversity, and what would it cost? Fuggedaboutit: we don’t have the time, much less the bucks. As Mora et al. note:

Considering current rates of description of eukaryote species in the last 20 years (i.e., 6,200 species per year; +811 SD; Figure 3F–3J), the average number of new species described per taxonomist’s career (i.e., 24.8 species, [30]) and the estimated average cost to describe animal species (i.e., US$48,500 per species [30]) and assuming that these values remain constant and are general among taxonomic groups, describing Earth’s remaining species may take as long as 1,200 years and would require 303,000 taxonomists at an approximated cost of US$364 billion. With extinction rates now exceeding natural background rates by a factor of 100 to 1,000 [31], our results also suggest that this slow advance in the description of species will lead to species becoming extinct before we know they even existed. High rates of biodiversity loss provide an urgent incentive to increase our knowledge of Earth’s remaining species.

Bob May isn’t as pessimistic: he think that the bulk of Earth’s species could be discovered within a century of fairly intensive labor, although even then we’re going to miss many species since they’re rapidly going extinct.  Mora et al. suggest where that labor should be concentrated:

. . .the bulk of species that remain to be discovered are likely to be small-ranged and perhaps concentrated in hotspots and less explored areas such as the deep sea and soil; although their small body-size and cryptic nature suggest that many could be found literally in our own ‘‘backyards’’ (after Hawksworth and Rossman [33]). Though remarkable efforts and progress have been made, a further closing of this knowledge gap will require a renewed interest in exploration and taxonomy by both researchers and funding agencies, and a continuing effort to catalogue existing biodiversity data in publicly available databases.

There are of course some potential problems with Mora et al.’s methods, and they do list them: they include uncertainty about how some taonomists define “species,” and the differential descriptive effort applied to different taxa. They also list problems with previous methods of estimating the number of species on Earth. I won’t go into this sort of detail since you can read the paper for free.

So why should we be cataloging all these species?  That’s what Bob May’s perspective is about, and he gives three reasons.  The first is because we can’t understand the evolutionary and ecological processes that create biodiversity unless we have a full understanding of the number of species.  I’m not highly convinced by this, because you can understand those processes simply by studying a smaller sample. There simply aren’t an infinite number of ways that new species can form.

The other two reasons are practical.  He argues that the number of species “underpins ecosystem services that . . humanity is dependent upon,” and that attempts to catalog biodiversity will invariably uncover some species that will be of tremendous aid to humanity.  (He uses the example of a new variety of wild rice that, when crossed to domesticated rice, improves output by 30%.  There is also the benefit for health, too: although May doesn’t mention this, a large proportion of the world’s pharmaceuticals ultimately trace back to compounds isolated from plants.)

For biologists like me, though, these economic considerations, while important, aren’t our real motivation.  We simply want to know what’s out there, for among those millions of undescribed species are millions of curious and interesting tales: things to inspire not only wonder about nature, but research and new knowledge, which is valuable for its own sake. Humans are a species permeated with curiosity, and satisfying that curiosity is a good in itself.  As I wrote in WEIT:

Each species represents millions of years of evolution, and, once gone, can never be brought back.  And each is a book containing unique stories about the past. Losing any of them means losing part of life’s history.

___________

Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. 2011. How many species are there on earth and in the ocean? PLoS Biol 9(8): e1001127. doi:10.1371/journal.pbio.1001127

Paula Kirby on evolution and faith

August 25, 2011 • 4:46 am

Two posts this early morning and then I’m outa here, but stay tuned.

In her latest “On Faith” column at The Washington Post, Paula Kirby answers the following question:

Q: Rick Perry, at a campaign event this week, told a boy that evolution is ‘just a theory’ with ‘gaps’ and that in Texas they teach “both creationism and evolution.” According to a 2009 Gallup study, only 38 percent of Americans say they believe in evolution. If a majority of Americans are skeptical or unsure about evolution, should schools teach it as a mere “theory”? Why is evolution so threatening to religion?

Kirby is a former Christian who once had dreams of becoming a nun, but gave all that up and is no longer inclined to pull her punches about religion:

Evolution is a simple fact. We can choose to remain ignorant of it, we can stick our fingers in our ears and refuse to think about it, we can even rail against it and shout and scream that it is not allowed to be true. But facts are facts, and will not go away just because we don’t like them. We don’t get to vote for our preferred method of having come into existence as a species, any more than we can choose to have been delivered by stork rather than conceived and born in the usual way. . .

She explains what a scientific theory is, and in the process gives a shout-out to both my book and Dawkins’s The Greatest Show on Earth (thanks, Paula!).

Kirby also doesn’t sugar-coat the problem that evolution poses for Christianity, and, having spent the last few weeks having my brain scrambled by theological attempts to show that of course God used evolution as his Preferred Method of Creation,  I appreciate Kirby’s contention:

While I welcome anyone who recognizes that the evidence for evolution is such that it cannot sensibly be denied, to attempt to co-opt evolution as part of a divine plan simply does not work, and suggests a highly superficial understanding of the subject. Not only does evolution not need to be guided in any way, but any conscious, sentient guide would have to be a monster of the most sadistic type: for evolution is not pretty, is not gentle, is not kind, is not compassionate, is not loving. Evolution is blind, and brutal, and callous. It is not an aspiration or a blueprint to live up to (we have to create those for ourselves): it is simply what happens, the blind, inexorable forces of nature at work. An omnipotent deity who chose evolution by natural selection as the means by which to bring about the array of living creatures that populate the Earth today would be many things – but loving would not be one of them. Nor perfect. Nor compassionate. Nor merciful. Evolution produces some wondrously beautiful results; but it happens at the cost of unimaginable suffering on the part of countless billions of individuals and, indeed, whole species, 99 percent of which have so far become extinct. It is irreconcilable with a god of love.

And this:

Christianity is like a big, chunky sweater. It may feel cozy, it may keep you warm, but just let one stitch be dropped and the whole thing unravels before your very eyes. Evolution is that stitch.

I have to refrain from just reproducing the whole column, but it’s really good—a shot fired across the bow of faith.

____________

UPDATE: At the same site, Richard Dawkins also has a piece attacking the ignorance of Rick Perry, and there are about twenty other pieces on the same topic by a variety of scientists, theologians, and intellectuals.


Peregrinations

August 24, 2011 • 1:03 pm

I’m off for vacation in California for about ten days starting tomorrow, so posting will be a tad lighter, though I will have internet access sporadically.  Matthew and Greg may fill in as well, though they’re busy as the school year looms.  Don’t, however, forget to scan your cats: entries are due on the last day of August.

Moar later.