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.

[Read more…]

A warehouse is burning in West Virginia

It’s been burning for almost a week. It’s owned by a “waste management company”, IEI, with a concept of “management” that involves stashing tons of old chemical waste in poorly maintained buildings with almost no documentation for Dupont. It’s basically producing a vast cloud of toxic fumes wafting over the state, and West Virginia is praying that the EPA will save them. Right. Scott Pruitt’s EPA. Although it can’t really be blamed on Pruitt, this is a situation that has been allowed to fester for decades — but you also can’t expect an incompetent know-nothing who favors the kind of laissez-faire corporate management practices that led to this situation to actually do anything about it.

There’s a terrifying collection of photos of the fire.

The warehouse used to be the Ames Factory (I think they made shovels there), but for years has been a dump for things that Dupont can’t legally get rid of. The state doesn’t know what was in there, but there is possibilities of any number of these products being stored there – PVC, Nylon, Carbon black, Titanium dioxide, Fiberglass, Maleic Anhydride TLV 0.1 ppm, Formaldehyde, PTFE (Teflon), Styrene, Acrylonitrile, Polybutylene Terephthalate, and/or Acrylic Sheet all of which are not good things when burned.

Edit: Update from Reddit “There is also an underground storage tank from when it was ames that is full of trichloroethyene, lead, ethylbenzene, and toluene that is leaking. The fire suppression system for the warehouse failed last winter because one of the pipes froze and busted. They never had it fixed.”

Edit 2: Another update from an insider that used to work for Dupont. IEI, who owns the building is a shell company owned by Dupont. Also, from a different insider “Saurabh Naik (Ed Note: The official owner of IEI) has dozens of LLC Shell companies like IEI that he funnels stuff through. He makes everyone that works from him sign an NDA. You’d be Shocked at some of the stuff that gets stored in his warehouses. You get everything from polymers to toxic Dust to drums of acid all thrown into the same sections of buildings. I’ve personally seen warehouses wall-to-wall with this stuff with literally no room to walk around in. If a Fire breaks out in one of his buildings then there is no way to put it out short of letting the entire thing Burn to the ground. Apparently this old AMES building was one of his worst and he’s already received many citations and Warnings about how things are stored and the general maintenance of the facility. Expect shutdowns of satellite warehouses soon and probably a couple bankruptcies declared as Well.”

Once again, West Virginia has gotten the short end of the stick when it comes to our water, air, and land. And because of this, our citizens are suffering and our fire fighters are risking their lives to help fight the fire.

This one is going to be a marketing challenge

There’s a new company with a dream: Fitbiomics. They aim to make a probiotics sports drink.

FitBiomics™ is a sports biotechnology company spinning out of the Wyss Institute for Biologically Inspired Engineering at Harvard University. We utilize next-generation sequencing to understand what makes elite athletes unique. In particular, we’re sequencing the microbiome of elite athletes to identify and isolate novel probiotic bacteria for applications in sports performance and recovery. We are purifying these novel probiotics and commercializing as ingredients to disrupt the sports nutrition market and cater to the next generation athlete.

Oooh. “Disrupt.” When the revolution comes and we truly disrupt the system, the people who use “disrupt” to describe peddling overpriced water are going to be among the first against the wall.

But hey, here’s a better translation from corporate-speak.

Certain bacteria show up more often in the poop of elite athletes than in the poop of sedentary people. So researchers theorized that a probiotic elixir containing components of elite athlete poop could help boost athletic performance and become the next hot sports drink.

Yeah. That’s going to be fun, selling Poopwater, the drink of champions.

Note, however, that they haven’t actually done any science to back up any claims of benefit. The guts of people who produce lots of lactate through exercise contain bacteria that thrive on lactate does not in any way imply that Dennis Kimetto’s performance is driven by his well-honed, skilled, disciplined poop.

Also, Fitbiomics looks rather dodgy. It doesn’t actually exist.

The Fitbiomics website lists Scheiman as CEO and Church, his mentor, as co-founder. To be more precise, Scheiman could become the CEO… if Fitbiomics gets funded. You see, Fitbiomics is not actually a company, at least not in the eyes of Harvard and the Wyss Institute. I stumbled on that surprise when I asked Mary Tolikas, Wyss Institute Director of Operations, why I couldn’t find any official disclosure of a financial interest on the part of Scheiman or Church (as distinct from their informal personal declarations).

“There is no company. There is no licensing agreement. There are no IP [intellectual property] assets or financial assets,” Tolikas said. She added that if they do seal a deal, they will move their work out of the Wyss Institute. Wyss Institute Administrative Director Ayis Antoniou also told me by email that faculty are required to disclose their financial interests and move their work out of the institute when they execute a licensing agreement with Harvard. “Prior to the financial interest being created, there is no conflict in the research activities under way, and thus no need for disclosures,” Antoniou wrote.

So it’s a placeholder website, with 10 employees, that has no scientific data backing up their premise, but this is apparently what the big name scientists are doing nowadays, corporatizing their results before they’ve got them.

Borrowing from evolution to create more efficient crops

Dang. I’m not a botanist, and I’m honestly a bit weak on all that plant stuff, but I have to give some background on plant anatomy and photosynthesis to give some context for this cool story. Fortunately I was explaining all this to students in cell biology last week, so I can manage!

First, you all know that plants make sugar from carbon dioxide and sunlight. They use photosynthesis in a set of light reactions to produce energy (in the form of reducing compounds and ATP) that are passed on to a pathway called the Calvin cycle, which fixes CO2 into carbon compounds. It does that by adding the carbon in CO2 to a 5-carbon sugar called ribulose bisphosphate, producing a 6-carbon molecule that is immediately split into two 3-carbon molecules, called 3-phosphoglycerate or 3PG. The enzyme that carries out this reaction is called rubisco, and it’s not particularly efficient. In fact, it’s kind of terrible — it works poorly in a low CO2 environment (like modern Earth!), and plants can lose 25% of their energy to a reaction with O2, rather than CO2. The Calvin cycle is thoroughly intertwined with all kinds of reactions in plant biochemistry, though, so it’s pretty much indispensible. There isn’t an alternative, more efficient reaction that can substitute for it.

Evolution has been creating workarounds, though! Some plants have evolved a kind of supercharger for CO2 — they use an alternative enzyme, PEP carboxylase, to fix CO2, adding the carbon to a 3-carbon intermediate, phosphoenol pyruvate, to produce a 4-carbon molecule, oxaloacetate, which is then passed along to other cells where the carbon is cleaved off to form CO2 again, which sounds kind of pointless, I know…except that what it does is create a CO2-rich environment in the destination cells, so rubisco can run much more efficiently. See? A turbocharger for plant sugar synthesis.

These plants also have a specific anatomical organization, called the Kranz (German for wreath) pattern. There is an outer ring of mesophyll cells that specialize in fixing carbon with PEP carboxylase, and they transport the 4-carbon intermediate into an inner ring of cells, the bundle sheath cells, where rubisco re-fixes the CO2 into a 3-carbon intermediate.

Not all plants have this ability. The plants that don’t, that rely entirely on just the bare bones Calvin cycle that produces a 3-carbon intermediate, are called C3 plants. Familiar C3 plants are wheat, rice, and barley. The plants that do have a supercharger and produce a 4-carbon intermediate are called C4 plants. Corn and sugar cane are well-known C4 crops. C4 is better at coping with environments poor in CO2, like everywhere. What if we could transplant that C4 metabolism in crop plants that lack it, like wheat and rice? We’d expect significant improvements in growth.

You might argue against that by noting that the Kranz anatomy is rather specific and detailed…but it turns out that Kranz anatomy is not essential for terrestrial C4 plant photosynthesis. Some plants have the C4 enzymes without the mesophyll/bundle sheath cell arrangement, and they benefit. It may also be feasible to engineer a proto-Kranz arrangement into C3 plants as a first step, and this is being done:

The C4 photosynthetic pathway accounts for ∼25% of primary productivity on the planet despite being used by only 3% of species. Because C4 plants are higher yielding than C3 plants, efforts are underway to introduce the C4 pathway into the C3 crop rice. This is an ambitious endeavor; however, the C4 pathway evolved from C3 on multiple independent occasions over the last 30 million years, and steps along the trajectory are evident in extant species. One approach toward engineering C4 rice is to recapitulate this trajectory, one of the first steps of which was a change in leaf anatomy. The transition from C3 to so-called “proto-Kranz” anatomy requires an increase in organelle volume in sheath cells surrounding leaf veins. Here we induced chloroplast and mitochondrial development in rice vascular sheath cells through constitutive expression of maize GOLDEN2-LIKE genes. Increased organelle volume was accompanied by the accumulation of photosynthetic enzymes and by increased intercellular connections. This suite of traits reflects that seen in “proto-Kranz” species, and, as such, a key step toward engineering C4 rice has been achieved.

Key things to note: they are recapitulating known evolutionary pathways to more rapidly ‘evolve’ a C3 plant to a C4 state. They’ve generated a line of rice with the first step in this pathway, the proto-Kranz condition. This does not, however, mean that they’ve produced a rice plant with higher yields — they have yet to introduce all the other steps in C4 metabolism. They do state that this transition, while not increasing efficiency yet, has also not reduced the yield of the rice plant, which suggests that the initial steps in the evolution of this pathway did not involve a cost to the plant, and also that the morphological changes, which I would have naively thought would be the biggest obstacle, may have been relatively trivial.

The complexity of the anatomical and biochemical changes needed for the C3-to-C4 transition appears seemingly incongruent with the multiple independent origins of the pathway. However, the results presented here suggest that one of the earliest steps in C4 evolution, the transition from C3 to protoKranz, could have resulted from modified activity of a single gene.

Now onward, to radically engineered biological organisms!

Voznesenskaya EV, Franceschi VR, Kiirats O, Freitag H, Edwards GE. (2001) Kranz anatomy is not essential for terrestrial C4 plant photosynthesis. Nature 414(6863):543-6.

Wang P, Khoshravesh R, Karki S, Tapia R, Balahadia CP, Bandyopadhyay A, Quick WP, Furbank R, Sage TL, Langdale JA (2017) Re-creation of a Key Step in the Evolutionary Switch from C3 to C4 Leaf Anatomy. Curr Biol. doi: 10.1016/j.cub.2017.09.040

Halloween carbs!

We have Cafe Scientifique on the last Tuesday of every month, which just happens to fall on Halloween this year. So we’re having appropriate content — come to the coffee shop, learn all about carbohydrates from Alyssa Pirinelli, and then go hand out carbs at home!

Not the ‘cell phones cause autism’ crap again

OMG, babies have thin skulls! They can be pierced!

That’s the kind of nonsense we get in bad popular science articles — a True Fact that is cited as demonstrating a real danger to children. Buzzfeed points to the sensationalist media hype over a terrible article that claims cell phones are warping babies innocent helpless brains.

The journal Child Development published what was described as a “review article” –an assessment of existing literature – by Cindy Sage and Ernesto Burgio. It was titled “Electromagnetic Fields, Pulsed Radiofrequency Radiation, and Epigenetics: How Wireless Technologies May Affect Childhood Development”, and was published in a “special section” of the journal addressing technology risks.

The paper got picked up by the UK national media. An article in the Express, published in May, asked: “Could wireless technology be causing MAJOR health problems in your children?”

It said: “Wireless mobile phones, laptops and tablets could be causing major health problems in children and contributing to autism and hyperactivity, a new study warns,” and said that these devices, “which even include baby monitors, emit radiation and electromagnetic fields that pierce thin skulls, harming memory, learning and other mental skills”.

However, a new paper published in the journal PeerJ by Dorothy Bishop, a professor of developmental psychology at the University of Oxford who specialises in developmental conditions such as autism, and David Robert Grimes, a medical physicist also at the University of Oxford, has issued severe doubts about the study. They said its claims are “devoid of merit” and “should [not be] given a veneer of legitimacy”.

The Child Development paper claimed that phones, Wi-Fi, and other sources of electromagnetic fields (EMFs) “are widely documented to cause potentially harmful health impacts that can be detrimental to young people”.

The actual article in Child Development isn’t quite that sensationalist, but it’s bad in other ways. As is usual in this kind of article about the horrors of electromagnetic radiation, I always wonder if, after they get rid of our cell phones, they’re planning to get rid of that great big thermonuclear-powered source of radiation and electromagnetic fields in the sky — after all, it’s silly to go after the piddling sources of feeble EMR while ignoring the many orders of magnitude greater zapper of rays that is bathing our whole planet in a seething stew of wavelengths and photons and rays and all that sciencey crap.

I wonder what the mechanism might be that causes autism in response to EMFs. This is always the problem with these kinds of ‘studies’ — they’re long on hypotheticals, and weak on the causal links that might be testable and might actually give some substance to the vapor. The Bishop and Grimes paper does a good job on dismantling their arguments there, too, because I was really annoyed when Sage and Burgio trot out their “Plausible Biological Mechanism for EMF/RFR Effects” and it’s…epigenetics. Epigenetics is the new buzzword that gets inserted in place of “magic” nowadays, and it’s getting obnoxious. You have to do real experiments and measurements of epigenetic phenomena to be able to make that claim — and simply noting that DNA repair is slower when your cells in culture are exposed to low-intensity non-thermal radiation, which might make them more prone to cancer, does not imply “epigenetics did it”. I don’t even know what they mean by epigenetics! It seems that whenever they observe an effect for which they have no causal mechanism, they just label it epigenetic and call that the mechanism, as if that explains anything.

Bishop and Grimes summarize it well.

Sage and Burgio make liberal use of epigenetic terminology, but in a nebulous and non-specific fashion, being deployed as an apparent deus ex machina to attribute negative health effects to WiFi in the absence of any evidence. Epigenetics is a term used to refer to the case where environmentally-induced modifications persist across generations, but Sage and Burgio treat it more as a synonym for gene-environment interaction. This usage is common among advocates of complementary and alternative medicine, but unhelpful as it confuses rather than clarifying the role of environmental effects.

Anyway, relax. There is no plausible mechanism for cell phones or WiFi to fry your baby’s brain, so go ahead, pierce their thin little skulls with radiation. I’m a big fan of holding babies close so that the infrared radiation you are emitting from your chest (more wattage than is coming out of your phone!) toasts their little heads with warmth. I think we humans have been doing that for a few hundred thousand years, so it’s probably not harmful. Probably. Studies pending.