We can predict that aliens exist, if aliens exist

I am informed that Oxford biologists have outlined what alien life would look like — I’m a bit put off by the title. One of those things that reduces the credibility of a story for me is when the editor feels the need to pump up the authority by prefixing “biologist” with the name of a prestigious university. Wouldn’t just “biologists have outlined what alien life would look like” been adequate?

I went ahead and read the source paper in the International Journal of Astrobiology, “Darwin’s Aliens”, and you know, I’m not very impressed. It claims in the abstract that “we can make specific predictions about the biological makeup of complex aliens,” but it doesn’t — it makes vague, amorphous generalities about possible aliens. Basically, it says that there would be replicators of some sort that would use natural selection, and then it announces that there would have been “major transitions” in their evolutionary history to generate complexity.

Uh, OK.

Picture an alien. If what you are picturing is a simple replicating molecule, then this ‘alien’ might not undergo natural selection. For example, it could replicate itself perfectly every time, and thus there would be no variation, and it would never improve. Or it might have such a high error rate in replication that it quickly deteriorates. If we count things like that as life, then there could be aliens that do not undergo natural selection. But if you are picturing anything more complex or purposeful than a simple molecule, then the alien you are picturing has undergone natural selection. This is the kind of prediction that theory can make. Given heredity, variation and differential success, aliens will undergo natural selection. Or, more interestingly, without those three things, aliens could not be more complicated than a replicating molecule. Given an adapted alien, one with an appearance of design or purpose, it will have undergone natural selection.

The telling phrase in there is this one:

This is the kind of prediction that theory can make. Given heredity, variation and differential success, aliens will undergo natural selection.

I agree. That’s the kind of prediction you can make. It’s kind of…broad, don’t you think?

Then they toss in their edifying zinger.

In particular, the evolution of complex life on the Earth appears to have depended upon a small number of what have been termed major evolutionary transitions in individuality. In each transition, a group of individuals that could previously replicate independently cooperate to form a new, more complex life form or higher level organism. For example, genes cooperated to form genomes, different single-celled organisms formed the eukaryotic cell, cells cooperated to form multicellular organisms, and multicellular organisms formed eusocial societies.

Who would have guessed? Complex organisms must have experienced increases in complexity in their evolutionary history.

You want another tautology?

Once again, picture an alien. If you are picturing something like unlinked replicating molecules or undifferentiated blobs of slime, then your aliens might not have undergone major transitions. But if what you are picturing has different parts with specialized functions, then your alien is likely to have undergone major transitions. What matters is not that we call them ‘major transitions’, but rather that complexity requires multiple parts of an organism striving to the same purpose, and that theory predicts that this requires restrictive conditions. Consequently, if we find complex organisms, we can make predictions about what they will be like.

If we find complex organisms, then we can predict what they will be like. You keep using that word, “predict”. I don’t think it means what you think it means.

Now we get an illustrative illustration of what an alien might look like.

Major transitions in space: ‘The Octomite’. A complex alien that comprises a hierarchy of entities, where each lower-level collection of entities has aligned evolutionary interests such that conflict is effectively eliminated. These entities engage in a division of labour, with various parts specializing on various tasks, such that the parts are mutually dependent.

Why? The authors seem to think that they can therefore predict that aliens will consist of a literal hierarchy of complexity, with literal morphological layers. I ask you, is there anything on Earth that looks like this? Then their model fails to predict any of the forms found on the one known planet with complex life, and is therefore rather pointless.

They have a summary of their method for making predictions.

When using evolutionary theory to make predictions about extraterrestrial life, it is important to avoid circularity. Our chain of argument is: (1) Extraterrestrial life will have undergone natural selection. (2) Knowing that aliens undergo natural selection, we can make further predictions about their biology, based on the theory of natural selection. In particular, we can say something about complex aliens – that they will likely have undergone major transitions. (3) Theory tells us that restrictive conditions, which eliminate conflict, are required for major transitions. (4) Consequently, complex aliens will be composed of a nested hierarchy of entities, with the conditions required to eliminate conflict at each of those levels.

I feel like I should remind you all that in their abstract, they say “we can make specific predictions about the biological makeup of complex aliens.” Those aren’t specific predictions. I don’t see how those generalities are at all useful in the task they’ve set themselves.

Also, nowhere in their model do they take into account the confounding variable of chance — it’s as if all they have to do is invoke natural selection and then the history of the species unfolds. Which it doesn’t.

Maybe that’s the point of highlighting the authors’ university — it’s supposed to make us overlook the bullshit.

I wonder how much he gets paid for these lies?

There is an EPA appointee, Robert Phalen, who is a researcher at UC Irvine. He has said some extraordinary things.

Speaking to the American Association for the Advancement of Science in 2012, Mr. Phalen told the audience: Modern air is a little too clean for optimum health. Mr. Phalen has also argued that the risks associated with modern particulate matter are very small and confounded by many factors. In a 2004 study, he wrote that, neither toxicology studies nor human clinical investigations have identified the components and/or characteristics of [particulate matter] that might be causing the health-effect associations.

No, really, he believes that.

Back in 2012, according to the American Association for the Advancement of Sciences (AAAS), Phalen claimed American children should be inhaling more pollution in order for their bodies to learn to handle it. According to a write-up on the AAAS official website, Phalen made the point bluntly.

Modern air is a little too clean for optimum health.

The article states further that Phalen described his most important role in science as causing trouble and controversy, and upon feeling an ocean breeze come through his office window, he remarked once again: See, the air is too clean.

This is what it takes to get a government appointment in the era of Trump and Pruitt.

Whole genome duplication in the house spider

Let’s talk about the evolution, development, and genomics of the common house spider. Yeah, it’s another YouTube video from yours truly.

Schwager EE, Sharma PP, and others (2017) The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 15(1):62. doi: 10.1186/s12915-017-0399-x.

Hilbrant M, Damen WG, McGregor AP (2012) Evolutionary crossroads in developmental biology: the spider Parasteatoda tepidariorum. Development 139(15):2655-62. doi: 10.1242/dev.078204.

No, your brain is not alive when you’re dead.
I feel stupider for having to write that.

Have you noticed this recent rash of truly stupid headlines?

I could show you many more, but that’s enough. None of that makes any sense! Some of the stories make it sound like your mind is trapped and screaming inside of your corpse after you’re dead, and none of it is true — it’s all an incredibly egregious distortion of what the paper actually says. I don’t know whether the ‘journalists’ were too stupid to comprehend the work, or they simply hadn’t read it so they were just making stuff up.

I read it, though. Here’s the summary:

Purpose of Review

Of the approximately 350,000 out-of-hospital, and 750,000 after in-hospital cardiac arrest (CA) events in the US annually approximately 5-9% and 20% respectively may achieve return of spontaneous circulation (ROSC) after attempted cardiopulmonary resuscitation (CPR). Up to 2/3 of these initial survivors may go on die in the subsequent 24-72 hours after ROSC due to a combination of (1) on-going cerebral injury, (2) myocardial dysfunction and (3) massive systemic inflammatory response. In order to successfully manage patients more effectively, monitoring methods are needed to aid clinicians in the detection and quantification of intra-cardiac arrest and post-resuscitation pathophysiological cerebral injury processes in the intensive care unit.

Recent Findings

Over the last few years many modalities have been used for cerebral monitoring during and after CA, these include quantitative pupillometry, transcranial doppler sonography, optic nerve sheath diameter measurements, microdialysis, tissue oxygenation monitoring, intra-cranial pressure monitoring, and electroencephalography. Current studies indicate that these modalities may be used for the purpose of neurological monitoring during cardiac arrest resuscitation as well as in the post-resuscitation period.

Summary

Multiple overlapping processes, including alterations in cerebral blood flow (CBF), raised intracerebralpressure, disorders of metabolism, imbalanced oxygen delivery and reperfusion injury contribute to cell death during the post-resuscitation period has led to the birth of post-resuscitation management strategies in the 21st century. This review provides a succinct overview of currently available bedside invasive and non-invasive neuro-monitoring methods after CA.

The rest of the paper consists of fairly detailed descriptions of various techniques of assessing the neurological state of dying patients. What it’s saying is that death isn’t like flipping off a light switch — there’s a progression of physiological changes over a short period of time, some of them irreversible, and many of them contributing to problems in prognosis if the patient is successfully resuscitated. None of this is surprising.

Unfortunately, the lead investigator, Sam Parnia, babbles somewhat outside of the content of the paper about near-death experiences and unconscious patients being able to witness what’s going on around them and the usual bullshit wrapped around confabulation. None of that is in the paper, though! It is kind of sleazy: say defensible, sober things inside a peer-reviewed paper, and then make up crap and pretend it’s supported by scientific research by association.

Niraj S, Parnia S (2017) Monitoring the Brain After Cardiac Arrest: a New Era. Current Neurology and Neuroscience Reports 17:62.

Exposing Christian inanity is a life-long calling

You know what really annoys me about creationists? The unwarranted confidence in their beliefs; the smug and almost always incorrect dismissal of the evidence; and the ridiculous repetition. There isn’t an original thought in their heads, so every discussion turns into yet another refutation of the same stupid talking points we dealt with last week, last year, last decade. Here’s an example, a letter the the editor of the Argus Leader by Jeff Hambek. He’s complaining about a previous letter from a <gasp> atheist.

He stated that he does not believe in an afterlife. Since that cannot be scientifically proven, this is an element of faith. Is there a way to establish the truth regarding afterlife? For the free thinker, the well-documented life, death and resurrection of Jesus present plenty of evidence that there is a soul or being that remains after death of the body.

Hang on there, Mr Double Standard. You dismiss the idea that there is no afterlife, because it “cannot be scientifically proven”, yet you immediately turn around and claim that the Jesus myth is evidence of an afterlife. This is a lie. There is no scientific proof, to turn your claim against you, of the life, death, and resurrection of Jesus. There isn’t even any contemporary evidence. It’s a religious fable packed with miracles and magic written decades after the claimed events.

On the other hand, we do have good scientific evidence that the mind is a product of activity in the brain. Damage to the brain causes, for instance, personality changes. We don’t have any evidence of human minds functioning without a brain. It’s reasonable to infer that the self does not survive brain death, and that there is no mental activity when the brain rots down into a putrescent puddle.

Mr Hambek is just getting started, though, and launches into a criticism of the science of the origins of life, and quickly demonstrates that he has no idea what he’s talking about.

The atheist must also believe that life in the universe began as a happy accident. Science cannot prove this either.

Chance and necessity, guy. Early chemistry was a stochastic process that depended on random events that produced a predictable outcome. Chemistry is not a series of “happy accidents”.

Consider that the chemistry of the early earth was not favorable to formation of amino acids (per NASA).

Huh. That’s weird. We find amino acids in meteorites, for instance. The early Earth was not favorable for formation of stable compounds when it was molten, but once it cooled enough for water to condense, amino acids would have formed. That part isn’t hard.

Even if there were amino acids,

There were amino acids, no “if” about it.

it is against the statistical odds that these would spontaneously form life-sustaining proteins, since only some amino acids will work and other chemicals combine more readily with amino acids than other amino acids.

Isn’t organic chemistry fun?

This odds-based argument is bunk, though. It’s not about chance at all. It’s about likely chemical pathways that would have been present in the pre-biotic earth.

Even if there were the right proteins, they would have to combine with other chemicals in just the right way to form a cell wall. The cell wall would have to be in the right place at the right time and enclose itself around the instruction manual (DNA) and power plant (mitochondria) necessary for the cell to live.

Early cells would not have had DNA or mitochondria. Mitochondria evolved a bit over 2 billion years ago, about 2 billion years after life arose. It’s also unlikely that the first cells would have had a cell wall — a cell membrane would have been assembled some time after the first autocatalytic processes evolved, but even that wouldn’t have come first.

I’m going to guess that Mr Hambek hasn’t read one book or paper about origin of life models.

No one has a reasonable explanation of how those things came into being by themselves.

Incorrect. See below.

Even if that very first cell were formed, it is an incredible leap from there to a multi-celled organism, which requires finely-tuned and interlocking systems to intake and distribute sustenance and dispose of waste.

Multicellular organisms aren’t as big a leap as Mr Hambek thinks. We all still use the same metabolic and replicative processes that evolved in prokaryotes, and even the cell signaling mechanisms that we’ve elaborated upon to produce greater complexity are present in single-celled organisms.

Atheistic religion was easier back in Darwin’s day. With what we now know about the chemistry and machinery inside a cell, I cannot muster the level of faith required for this religion.

Oh god, here we go again — a religious believer using a claim that atheism is a religion as a pejorative, and using the same old slogans I’ve heard for forty years. Please learn a new routine.

I’m going to have to recommend some remedial reading for Mr Hambek. Here’s a paper on Early bioenergetic evolution by, among many others, Martin and Lane. It kinda contradicts a lot of his half-assed claims about the science.

Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood–Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type ‘reduced iron → reduced carbon’ at the beginning of bioenergetic evolution.

Chemistry ain’t a religion, OK?

That paper might be too technical for someone who gets his ‘facts’ out of a Bible, so here’s a less complicated discussion of some possible 4 billion year old fossils.

Discovered in slices of rock recovered from northern Quebec, the microscopic metallic detritus—plus chemical signatures associated with ancient metabolisms—could push back the date at which life arose on Earth. If verified, these fossils would surpass 3.7-billion-year-old microbial mats found in Greenland as the oldest known traces of life.

The microfossils also lend support to the idea that the warm, watery, mineral-rich neighborhoods around submerged vents are prime places for life to emerge, whether on this planet, on the seafloors of icy moons, or elsewhere in the universe.

Scientists seem to think the emergence of life is probable, not just a “happy accident”. But who are you going to believe, a bunch of people who’ve studied chemistry and biology for years, or some random Christian doofus from South Dakota who doesn’t even realize that not all cells have mitochondria?

A little video about sex determination

I read this paper:

Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP, Ashman TL, Hahn MW, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Valenzuela N, Vamosi JC (2014) Sex determination: why so many ways of doing it? PLoS Biol. 12(7):e1001899.

And now I give you a quick summary of a couple of figures that I know you’ll find useful if you’re teaching genetics.

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