Graaarh, physicists BIOLOGISTS

I thought physics was the most hubristic scientific discipline of them all, but I may have to revise that assessment. Last week I was sent another of those papers published in archiv, the physics repository, making grand pronouncements about evolution, and I made the mistake of simply dismissing it on twitter — it was simply too ridiculous to post about. But now io9 has picked it up, and more people are clamoring at me to explain it.

Jebus, it’s terrible.

Here’s what Sharov and Gordon claim:

An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a nucleotide. The genetic complexity, roughly measured by the number of non-redundant functional nucleotides, is expected to have grown exponentially due to several positive feedback factors: gene cooperation, duplication of genes with their subsequent specialization, and emergence of novel functional niches associated with existing genes. Linear regression of genetic complexity on a log scale extrapolated back to just one base pair suggests the time of the origin of life 9.7 billion years ago. This cosmic time scale for the evolution of life has important consequences: life took ca. 5 billion years to reach the complexity of bacteria; the environments in which life originated and evolved to the prokaryote stage may have been quite different from those envisaged on Earth; there was no intelligent life in our universe prior to the origin of Earth, thus Earth could not have been deliberately seeded with life by intelligent aliens; Earth was seeded by panspermia; experimental replication of the origin of life from scratch may have to emulate many cumulative rare events; and the Drake equation for guesstimating the number of civilizations in the universe is likely wrong, as intelligent life has just begun appearing in our universe. Evolution of advanced organisms has accelerated via development of additional information-processing systems: epigenetic memory, primitive mind, multicellular brain, language, books, computers, and Internet. As a result the doubling time of complexity has reached ca. 20 years. Finally, we discuss the issue of the predicted technological singularity and give a biosemiotics perspective on the increase of complexity.

Life originated 9.7 billion years ago, huh? Maybe 13 billion plus years ago? I didn’t even have to read the paper: I predicted that there would be a certain graph in it, opened it up, scanned to Figure 1, and there it was.

dumbassgraph

We’re done. Anyone else see the problem?

They cherrypicked their data points. They didn’t include lungfish, ferns, onions, or some protists because that would totally undermine their premise; those are contemporary organisms with much larger genomes than mammals’, and their shallow, stupid exercise in curve-fitting would have flopped miserably. It’s a great example of garbage in, garbage out.

There’s another figure, in which they slap their ‘origin of life’ numbers on a diagram of the history of the universe. Very convincing. I could also stick a label on such an image and show the ‘origin of clowns’ at the time of the Big Bang. It wouldn’t make it scientific, though.

sillyorg

Do they have any other evidence to support their claim? No, not one bit. Most of the paper is a handwavey summary of various models of abiogenesis, with no effort to be quantitative…except for their quantitative claim on the basis of one fudged graph that life originated over 9 billion years ago. There’s also some weird stuff about biosemiotics, which they use to argue for goals and meaning in evolution. It seems to be a popular term among creationists, and what little I’ve read on it from marginally more credible sources makes it look like nonsense.

That graph, though, just kills it. At least try to respect the larger data set, will ya, guys?

This was published in archiv, probably to escape the restrictions of peer review (i.e., slip some bullshit under the door), and really, I read that and thought, “physicists, again?” But then I looked closer at the authors. I am so ashamed.

Alexei A. Sharov, Ph.D.
Staff Scientist, Laboratory of Genetics
National Institute on Aging (NIA/NIH)

Richard Gordon, Ph.D.
Theoretical Biologist, Embryogenesis Center
Gulf Specimen Marine Laboratory

They’re biologists of some sort. Now I have to crawl off in embarrassment for my discipline.

The Genetic Code is not a synonym for the Bible Code

Oh, boy. The Intelligent Design creationists are all excited about a new paper that purports to have identified an intelligent signal in the genetic code.

Here’s a new paper that can be added to the growing stack of intelligent-design articles in peer-reviewed journals. Even though the authors do not use the phrase “intelligent design,” their reasoning centers on the detection of an intelligent signal embedded in the genetic code — a mathematical and semantic message that cannot be accounted for by a natural cause, “be it Darwinian, Lamarckian,” chemical affinities or energetics, or any other.

I’ve read the paper by ShCherbak and Makukov, and by golly, the Discovery Institute flack really has accurately summarized the paper: it does explicitly and clearly claim to have identified evidence of design in the genetic code! That’s newsworthy in itself, that the creationists can accurately summarize a scientific paper…as long as the results conform to their ideological expectations.

Unfortunately, what they’ve so honestly described is good old honest garbage.

Here’s the short summary of what they do: they jigger the identities of the amino acids coded for by each codon into a number, a nucleon sum. What is that, you might ask? It’s determined by adding up the number of protons and neutrons in the amino acid, which is simply the mass number of the compound. Further, you can distinguish the amino acid into it’s R group, and the atoms that make up the peptide chain proper, which he calls the B group, for standard block. The mass number of the B group is always 74, except for proline, so he transfers a hydrogen from the R group to the proline B group to bring it up to 74, and by the way, did you notice that 74 is two times 37, which is a prime number? Now if you take all the three-digit decimals with identical digits (111, 222, 333…999), and sum their digits (111=3, 222=6, 333=9, etc.) you get the quotient of the number divided by…37!!!1!!

Are you impressed yet? This is simply numerology, juggling highly derived quantities that have little to do with functional properties of the molecules to come up with arbitrary numerical relationships, and then claiming that they’re somehow significant. They also play games with the sums of the mass numbers of just the R groups for certain codons, adding or subtracting the B number, finagling things until they get numbers that are evenly divisible by their magic prime number of 37, etc. It’s pure nonsense through and through.

But every once in a while, something sensible emerges out of the murk. Here’s the logic of their argument:

To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features, but they should be inconsistent in principle with any natural process, be it Darwinian or Lamarckian evolution, driven by amino acid biosynthesis, genomic changes, affinities between (anti)codons and amino acids, selection for the increased diversity of proteins, energetics of codon-anticodon interactions, or various pre-translational mechanisms.

(1) is simply saying that there must be a pattern of some sort — if the code were purely random assignment of arbitrary nucleotides to each amino acid, it wouldn’t be much of a sign — it would suggest that the sequence is noise, not signal. (2) is the really hard part, the one where you’d have to do a lot of work: you’d have to show that natural processes did not contribute to the pattern. They do not do that. They can’t do that. They take a different and curious tack.

They literally argue that because organizing the code by their nucleon sums makes no sense and has no reasonable functional consequences…therefore it must be an artificial and intentional feature. I’ve heard this argument before. It’s called the Chewbacca defense. Ladies and gentlemen, think about it: that does not make sense! If nucleon numbers show a mathematical pattern of any kind in their relationship to codons, you must accept the existence of a designer.

However, if we can show a natural property that leads to the organization of the genetic code, then I’m afraid their argument evaporates. Even more so than building an argument on the Chewbacca defense, that is.

There’s a very good discussion of the genetic code in Nick Lane’s book, Life Ascending: The Ten Great Inventions of Evolution, and I’ll briefly summarize it.

First, there is a pattern to the genetic code! No one has ever denied that; it’s obviously not the case that amino acids are randomly assigned to trios of nucleotides. Here’s the code:

geneticcode

Let’s look at one amino acid, glycine (Gly), down in the bottom right corner. The genetic code is degenerate: that means that most amino acids have multiple combinations of nucleotides that can specify them. Glycine’s codes are GGU, GGC, GGA, and GGG. Do you see a pattern? The code is actually GG_, where the third position has a lot of slack or wobble, and any nucleotide will do. We see similar cases where just the first two nucleotides are sufficient to specify leucine, valine, serine, proline, threonine, alanine, and arginine. Even with the other amino acids, there are some constraints; CA_ can identify histidine or glutamine, but if the third letter is a pyrimidine (U or C), you get histidine, while if it’s a purine (A or G), you get glutamine. There are patterns all over the place here! So of course ShCherbak and Makukov could find evidence of significant organization.

But there’s more. There are other rules associated with this pattern.

In the synthesis of these amino acids, biochemistry typically modifies a raw starting material. The first letter of the codon says something about the biosynthesis of the associated amino acid.

If the first letter is:
• C, then the amino acid is derived from alpha-ketoglutarate.
• A, then the amino acid is derived from oxaloacetate.
• T, then the amino acid is derived from pyruvate.
• G, then the amino acid is derived in a single step from simple precursors.

The second letter of the codon is correlated with chemical properties of the amino acid.

If the second letter is:
• A, then the amino acid is hydrophilic.
• T, then the amino acid is hydrophobic.
• G or C, the amino acid has an intermediate hydrophobicity.

Wait…so there’s a pattern to the genetic code, and that pattern is associated with the physical properties of the amino acids? Why, that makes sense. Chewbacca is routed! The most likely origin of the code lies in likely catalytic properties of dinucleotides; pairs of nucleotides in ancient organisms were initially functioning as proto-enzymes before they were incorporated into strings of coding information. At least that provides a historical physico-chemical route to the particular code we now have that does not require weird numerological masturbation.

It’s rather pathetic that the Discovery Institute thinks this is a beautiful piece of science. It’s not. It’s nonsense. But look how the DI spins this story:

How will evolutionists respond to this paper? It’s hard to see how they could dismiss it. Maybe they will try to mock it as old Arabian numerology, or religiously inspired (since Kazakhstan, which funded the study, is 70% Muslim). Those would be unfair criticisms. The authors have Russian names, certified doctorates, and wrote in collaboration with leading lights in the West. Or perhaps critics could argue that the authors hail from a foreign country whose name has too many adjacent consonants in it to take them seriously.

No, it appears the only way out for Darwinists would be the “Dawkins Dodge.” You may remember that one from the documentary Expelled, where Dawkins admits the possibility of panspermia for Earth, so long as the designers themselves evolved by a Darwinian process.

What’s most notable about this paper is the similarity in design reasoning between the authors and the more familiar advocates of intelligent design theory. No appeals to religion or religious texts; no identifying the designer; just logical reasoning from effect to sufficient cause. The authors even applied the “design filter” by considering chance and natural law, including natural selection, before inferring design.

If Darwinists want to go on equating intelligent design with creationism, they will now have to take on the very secular journal Icarus.

I didn’t even consider the religious or ethnic basis of this study; it didn’t come to mind at all. It is clearly simple stupid numerology, though. Look at the rationale given for all of the conclusions, which consist entirely of mathematical manipulations of arbitrary derived properties of the molecules, to arrive at a claim of prime number significance.

We certainly don’t need to invoke panspermia. Nothing in the genetic code requires design. and the authors haven’t demonstrated otherwise.

I am most amused by the cute parallelism of claiming surprise that the authors of this paper use “design reasoning” similar to that used by American Intelligent Design creationists. They’ve been slinging this slop for decades; why be impressed that another set of Intelligent Design creationists in Kazakhstan are using the same tired tropes?

I’m also not impressed with the failure of implementation of their logic. OK, they have a ‘design filter’ that they apply, but so what? Their methods failed to recognize a well-known functional association in the genetic code; they did not rule out the operation of natural law before rushing to falsely infer design.

And that last bit…I don’t care what journal it was published in. The prestige of a journal does not confer infallibility, and even the best of journals will occasionally publish crap. They will be especially likely to publish garbage when they stretch beyond the expertise of their reviewers. Icarus is a journal of planetary science that publishes primarily on astronomy and geology. This particular paper conveniently falls between the cracks — it’s a weird paper full of trivial arithmetical manipulations for arcane purposes with no scientific justification for any of its procedures. I don’t know how it got accepted for publication, other than by boring the reviewers with its incomprehensible digit fiddling.

One last thing: don’t rush to claim a secular purpose behind this work. It’s already been appropriated by freaky strange religious fanatics and lovers of the bible codes. You can’t blame shCherbak directly for this weirdo’s interpretations, but certainly he isn’t far from his temperament.

The facts presented on this site, when combined with those now revealed to us by shCherbak, constitute invincible evidence of the truth of the Judeo-Christian Scriptures, and of the Being and Sovereignty of their Divine Author.

Yeah, numerology. Nothing but wanking over tables.

Larry Moran has more — it turns out that Uncommon Descent and Cornelius Hunter also liked this paper. Flies are drawn to shit, I guess.

Terraforming the easy and fun way with desert plants

I spend a lot of time paying attention to threats to the organisms that live in the desert, and what with all the environmental bad news available online these days that can be pretty damned depressing. This past weekend, though, I was reminded that there is actually hope for the future. Centuries from now we may well find that desert plants, especially those that now live within a day’s drive of Los Angeles, have a vital role to play in making yet-undiscovered planets habitable.

I was reminded of this while re-watching a set of documentary films describing the terraforming of an entire complex system full of dozens of more or less habitable planets, in many cases using entire vegetative suites once native to the California desert. I’ve gone back and taken some screenshots of these films to illustrate some of the ways in which the terraformers used desert plants, and they — along with discussion of the terraformed vegetation –are below the fold.

[Read more…]

They’re coming to get you, Chandra!

The crackpot wing of the astrobiology community (and I do know, there are rational and scientific members of that group!) has now flowered into full-blown paranoia. N. Chandra Wickramasinghe has published a remarkable paper on arXiv titled Extraterrestrial Life and Censorship, which isn’t as much a review of the evidence as a personal recounting of the global conspiracy to silence people who claim to have evidence of extraterrestrial life. It’s a bizarre piece of work that has the keywords “Dark
Matter;
Planet
Formation:
Cosmic
structure;
Astrobiology”, when it’s not really about any of those things; the keywords should have been “MenInBlack; They’reComingToTakeMeAway; Fools!I’llTeachThem”.

It’s strange to see Wickramasinghe constantly refer to his critics as “frightened” and characterize them as “scared out of their wits”. I have no idea what he thinks they are afraid of; he even begins the paper noting that there is nothing scary about astrobiology.

The ingress of alien microbial life onto our planet, whether dead or alive should not by any rational argument be perceived as a cause for concern. This is particularly so if, as appears likely, a similar process of microbial injection has continued throughout geological time. Unlike the prospect of discovering alien intelligence which might be justifiably viewed with apprehension, the humblest of microbial life-forms occurring extraterrestrially would not constitute a threat. Neither would the discovery of alien microbes impinge on any issues of national sovereignty or defence, nor challenge our cherished position as the dominant life- form in our corner of the Universe.


And then, with a complete lack of awareness of what he has just written, he goes on to assert that every one of his critics is terrified. Of what, I wonder? He almost gets the answer.

After 1982, when evidence for cosmic life and panspermia acquired a status close to irrefutable, publication avenues that were hitherto readily available became suddenly closed. With the unexpected discovery that comets had an organic composition, with comet dust possessing infrared spectra consistent with biomaterial attitudes hardened to a point that panspermia and related issues were decreed taboo by all respectable journals and institutions.


The peer review system that was operated served not only to exclude poor quality research but also to deliberately filter publication of any work that challenged the standard theory of life’s origins.


I’ve highlighted the important phrase there. One of the functions of peer review is to set certain standards and make a preliminary sorting of the wheat from the chaff. When you’ve got two explanations, one being that the work is excluded for its poor quality and the other being that there is active censorship of work the editors fear, and you’ve opened your paper by explaining that there is nothing to fear from astrobiology, doesn’t that imply that the first explanation is better?

As another indicator that Wickramasinghe is trying to publish garbage, I notice that throughout his paper he is remarkably incapable of noticing that “organic” and “biological” are two different words. Finding organic compounds is not evidence of biological activity.

Amazing gibberish

Renew America, the bizarrely, deeply, weirdly conservative web site founded by Alan Keyes, really had to struggle to find someone crazier than Pastor Grant Swank and Fred Hutchison and Bryan Fischer and Wes Vernon (let alone Alan Keyes himself), but they have succeeded. They have Linda Kimball writing for them. She has written the strangest history of evolutionary biology ever — I think she was stoned out of her mind and hallucinating when she made this one up. It’s called “Evolutionism: the dying West’s science of magic and madness“. The title alone is enough to hint at the weirdness within, but just wait until you read where evolution comes from.

Though taught under the guise of empirical science, naturalistic evolution is really a spiritual concept whose taproot stretches back to the dawn of history. It was then, reports ancient Jewish historian Josephus, that Nimrod (Amraphel in the Old Testament) used terror and force to turn the people away from God and toward the worship of irrational nature. Moving forward in time to the Greco-Roman world, evolution serves as the mechanism of soul-transference in metempsychosis and transmigration of souls. In the ancient East, the mystical Upanishads refine evolution and it becomes the mechanism of soul-movement in involutions, emergences, incarnations, and reincarnation. In that both rationalist/materialist/secularism and its’ counterpart Eastern/occult pantheism are modernized nature pseudo-religions, it comes as no surprise that evolution serves as their ‘creation mythos’.

It’s a little surprising that Josephus isn’t regarded as a member of the Greco-Roman world, but I had no idea that I was teaching about metempsychosis and reincarnation. The students are going to be really shocked when I put that on the exam next year.

Kimball’s grip on the history of the last century is no better than her understanding of prior millennia, either.

Today, in addition to original Darwinism — which many scientists have already rejected as useless — there are three other versions of Naturalist evolutionism: neo-Darwinism, punctuated equilibrium, and panspermia, the notion that life was seeded on Earth by highly evolved beings either from another planet, or from another dimension. The latter two versions are favored by powerful Transnational Progressive New Age occult insiders such as Marilyn Ferguson, Robert Muller and Barbara Marx Hubbard as well as by channeling cults who are excitedly ‘receiving revelations’ from discarnate entities calling themselves the Space Brothers, the Council of Nine, Transcended Masters, and more recently, the ancient Ennead of Egypt.

Uh, neo-Darwinism is Darwinism with genetics and population genetics; it’s an evolution of the original theory proposed by Darwin. Punctuated equilibrium is a much narrower subset of evolutionary theory that describes the distribution of observable change in a fossil lineage. It’s nowhere near the same footing or the same scope as neo-Darwinism.

Panspermia isn’t even on the radar.

How come the Space Brothers, the Council of Nine, Transcended Masters, and the ancient Ennead of Egypt never show up at any of the biology conferences I attend (is anyone else confused by the conjunction of “recently” with the ancient Ennead)? And they never publish!

Then there are the conspiracy theories. You knew there had to be conspiracy theories.

Whereas occult pantheism quietly flowed beneath ‘red-colored’ atheist-materialist-communism and Nazism during the twentieth century, that order is quickly reversing. Today, ‘green-colored’ occult pantheist-socialism is brazenly striding onto the world-stage in full public view while materialist-secularism slowly fades to black. Already, zealous High Priests and Priestesses of the occult arts are calling the U.N the world church and the world mind, while other madmen such as David Spangler, demand that everyone submit to a satanic-initiation to qualify for entry to the coming green New World Order.

Back away slowly, everyone. This one needs the tranq gun and the rubber room.

She seems to have confused us godless atheistic materialist evilutionists for a bunch of New Age wackaloons. And her bottom-line message is that we have to prop up good old Christianity, because otherwise the tree-worshipping Satanists are going to take over.

An amusingly suspicious “paper”

There is a site called ScienceBlog, at scienceblog.com. Note that it is a little different from scienceblogs.com — it lacks the “s”. There are a few other differences, too: it’s a site that simply reprints press releases. Send ’em anything, and they’ll spit it back up on the web for you.

One such example is a press release titled Life on Earth came from other planets. It purports to be a summary of a peer-reviewed, published research paper.

This one:

“Life on Earth Came From Other Planets,” by R. Joseph, Ph.D. Cosmology, Vol 1. 2009.

There are a few funny things about this article. The journal Cosmology doesn’t seem to exist. Then notice “Vol. 1″…this is the inaugural issue. It contains a grand total of one (1) paper, the aforementioned article by Rhawn Joseph.

Wait! It does exist! The “journal” exists as a web page only; go ahead, here’s Cosmology, 2009, Vol 1, pages 00000. You can read the whole article, which you know was peer reviewed, because it says so in the upper left corner: “Peer Reviewed”.

Guess who the web page can be traced to? Rhawn Joseph.

I think you begin to see a pattern here. If you can’t get your crappy paper published in a legitimate journal, invent one!

The comments at scienceblog.com are hilarious, too. To his credit, the author of the site, Fred Bortz, shows up to offer objections to the weird quality of the submission; someone named Joy Haiyan Wu, who works with Rhawn, pops up a few times to complain and threaten legal action. A comment by Christopher Coffee pretty much nails the phoniness of the whole effort.

What about the paper itself? Complete garbage. It presents nothing new, makes exaggerated claims about the likelihood of bacterial life surviving in space for hundreds of millions of years (it wouldn’t), makes grand claims of revolutionizing our understanding of the origins of life, and offers nothing other than rehashed claims and denial of legitimate scientific hypotheses. You can get a taste of how poor this paper is from just the conclusion.

Life on Earth appeared while this planet was still forming. There is no proof life can be created from non-life. As only life can produce life, only panspermia is a viable scientific explanation as to the origin of Earthly life. The first life forms to appear on Earth were produced by other living creatures who were likely encased in debris ejected by the parent star nearly 5 billion years ago.

Well, life had to have come from non-life at some point, logically speaking. The claim that only life can produce life clearly had to have been wrong at some point, and panspermia doesn’t get around the fundamental problem: where did the life at that distant exploding star come from?

I haven’t even mentioned yet that the writing is incoherent and poorly organized, the paper is full of typos, and although it contains many citations, the references have been left off…and instead we get a repetition of ten ads flogging Rhawn Joseph’s self-published book.

I look forward to issue 2 of volume 1 of Cosmology. Perhaps it will have another paper by Rhawn Joseph?

How Life Began

As I said I would, I’m watching this History Channel documentary about the origin of life. How about a little live-blogging?

8:00. Ugh. It begins with a bunch of tripe from Coyne and Polkinghorne, claiming we need religion to understand the meaning of life. This is a bad, bad start, but I’m hoping it’s nothing but a weasely preliminary that they will then abandon to get to some real science.

There are lots of gimmicky special efects, but OK, let’s get the general audience interested. I’m not too keen on the parade of talking heads, though: they keep trotting out different investigators, letting them say a sentence or two, and then zipping off elsewhere. I know you don’t want some guy sitting and droning at you, but this seems like a poor compromise.

8:15. It’s a quick tour of the complexity of the cell. They’re using this special effects analogy of a “factory of life” where chemistry is going on.

First important element of life: metabolism. Second: life is cellular, with compartments. Third: life can replicate.

Now we get a parts catalog of polymers: lipids, proteins, and nucleic acids.

Very weird: in their factory analogy, they point to something hidden behind a big red curtain and say that that’s where all these bits and pieces come together to make something that’s alive; it seems a bit of a cop-out, a way to pretend there’s something hidden where the viewer can imagine anything they want. Come on, bite the bullet and admit it: life is chemistry, and there is nothing more.

Now we get a fairly lengthy discussion of the idea of emergence. At least they clearly state that emergence is nothing magical, but is just a consequence of the execution of the laws of nature. This is a rather pointless digression, I think.

OK, now we get a timeline of the origin of life: it appeared about 3.8 billion years ago, on a very hostile planet with no oxygen in the air, and just cooling after the last of the great meteor bombardments. This leads naturally into a discussion of extremophiles, with a tour of Mono Lake.

Segue to commercial by mentioning that life will change the environment of the earth.

8:30. Conditions on early life are hostile to us, but chemical energy is abundant. Life would have existed as single-celled forms only, which may have been unrecognizable to us (why are they showing video micrographs of nematodes while they tell us this?)

Stromatolites are introduced, as organisms that grew on chemical energy sources. What are those energy sources?

The camera crew goes spelunking. They’re collecting rock-eating microbes, which the scientists argue is a kind of primitive chemistry that evolved before photosynthesis.

Nice reminder that single-celled life was the only form of life here for 80% of the history of earth, but then they make the mistake of using the past tense in saying they were the dominant form of life on the planet.

Wait…now they’re saying that the ability to reproduce is a property of DNA? That’s kind of cutting off the possibility of an interesting discussion of alternative paths.

Suddenly, boom, they’re talking about Leeuwenhoek. Hang on, this is a bit jumpy. Can we talk more about extremophile chemistry before we start on 17th-18th century microscopy?

Now it’s all about photosynthesis. We’ve moved way, way beyond the period of early abiogenesis already, and they’ve scarcely touched on any of the major theories.

Before the commercial, we get talk about multicellularity and oxygen chemistry. Either they’re going to be jumping about an awful lot and scrambling the story, or we’re not going to get anything about abiogenic chemistry…

8:45. Oops, I had to miss part of this section to run some real-world errands. I come back to see the Burgess Shale and a discussion of the Cambrian explosion. This is long, long after the origin of life!

It’s an excuse to show some computer animations of Anomalocaris, anyway.

George Coyne does a good job now saying that life doesn’t need a designer; Polkinghorne pops up to make excuses for the metaphorical nature of the book of Genesis. Bugger off, Polkinghorne, you bother me, ya twit.

Now we get a summary of the importance of selection and sex. I don’t think we’re going to get a good review of biogenesis anymore — sex is not an important issue in that field.

I am completely baffled. Before the commercial, they say the big question was how human life arose…then they ask, “What was the specific mechanism that caused non-living chemistry into living biology?” Weird. These are very different questions. They seem to be muddling up the origins of life with the origins of the only important form of life, humans.

9:00. We’re back to animals. Come on, animals are peculiar latecomers.

Maybe it’s an excuse to return to a historical survey of ideas about the origin of life. I hope.

Aristotle proposes the idea of spontaneous generation, an idea that hangs on for centuries but is relatively easy to disprove…as Redi and Spallanzani do. This stuff isn’t bad, but it feels like introductory material they should have brought up at the beginning.

Actually, I’m enjoying this part best of all so far. They’re actually talking about the experiments done to disprove spontaneous generation, so it’s a useful summary of how scientists actually do science.

Our closing question: so how did life arise from chemistry? The second half is off to a good start, I think.

9:15. I’ve got to say…the actor playing Charles Darwin looks nothing like him, and that beard looks cheesy and fake.

We get the early concepts: “warm little pond”, “primorial soup”. There the questions are about what kind of chemicals and conditions existed at the beginning of life. They mention Oparin’s ideas about the chemical monomers available, and the idea that these chemicals would accumulate in the oceans. It seems like a very low probability sort of exercise.

The Miller/Urey experiment at last. This is well done, with a very nice illustration of the apparatus and techniques. They get it right, too — it was nice work that showed that the natural chemistry that would produce organic substrates for life was relatively trivial. It also set up unrealistic expectations for how easy it would be to create life.

Closing premise: now there is a race to figure out prebiotic chemistry.

9:30. Let’s consider other sources of organic matter!

Space-borne debris. Complex organic molecules are found in metorites and in space. We get to see scientists extracting organic molecules from ground-up meteorites. Panspermia is mentioned, but they aren’t doing a good job of distinguishing chemicals from life. At least Bob Hazen is razor sharp in pointing out that panspermia is a cop out.

Hazen also clearly explains bottom-up (exploring basic principles about biochemistry to replicate the events at the origin) vs. top-down (working in reverse from extant life backwards to the origin). He also explains that we need a multiplicity of approaches, and the origin may also have been generated from diverse sources.

Hmm. Commercials seem to be coming more frequently as we get close to the end.

9:40. It’s deep-sea vent time, with nice shots of black smokers and squid. Then Bob Hazen shows us how his experiments on the chemistry at high pressure and temperature are done. Cooking a little pyruvate for a while generates substances that form micelles.

Clays! Clays are shown as potential catalytic surfaces that would concentrate organic compounds and promote reactions that form, for instance, RNA. RNA monomers will polymerize in the presence of clays.

Transition: are scientists on the verge of creating artificial life in the lab?

9:50. It’s “3000 years after Aristotle”? What?

Never mind. Now we get pretty crystals growing and changing. This bit is a little fluffy.

All right: Jack Szostak. They describe his efforts to try and create a protocell. Cool video of creating cell membranes — beautiful little droplets bubbling out of an electrode. Some good cautionary statements: if they succeed, this will still only be a model, not a demonstration of how it actually happened 3.8 billion years ago.

They don’t really say much about the mechanisms in the closing minutes, but they do have a nice statement by Neil de Grasse Tyson about how the search is the important thing, even if we don’t get an answer.

Summary: the first hour was a muddle, and not worth watching. If you’re going to catch it later, just watch the second half.

The last half wasn’t bad. It at least talked very briefly about the actual science and how it is done. It was all painfully abbreviated and only touched lightly on the subject, but I think that is simply a limitation of the medium. I imagine it’s a seriously difficult balancing act to try and meet the needs of real nerds (like us!) and the more casual viewer, so I’ll accept the compromise.

Something at the end to lead the interested viewer to more in-depth sources would have been a good idea — they could have at least mentioned Hazen’s Genesis as a plug.

Tom Bethell cries

Russell Seitz discovers another review of Expelled. It’s by that deluded dolt, Tom Bethell, and it’s a positive review.

It is surely the best thing ever done on this issue, in any medium. At moments it brought tears of joy to my eyes. I have written about this controversy for over 30 years and by the movie’s end I felt that those of us who have insisted that Darwinism is a sorry mess and that life surely was designed are going to prevail.

Deluded much? If he were at all aware of the science of biology, he’d know that evolution is not going anywhere but deeper into explaining life on earth. A propaganda film cannot change the science, although it could, if it were better done, change the culture in damaging ways.

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