Bad Science+Bad Journalism=Bad Publicity

It is unusual how press-conference-quality-science often doesn’t meet the qualifications of undergraduate-quality-science. Examples of this include Ida, arsenic DNA, vaccines cause autism; I could go on, but you get the idea. All of these have several things in common, many things wrong, and interesting lessons. These are important for many reasons, but mostly because, even with bad science, we can learn from them.

Ida-that delightful little Darwinius masillae fossil from the Messel pit in the southwest corner of the state of Hesse in Germany-was a gorgeous fossil, and could have been even more remarkable had it been properly studied without trying shoehorn this little fossil as a transitional form between Strepsirrhini and Haplorhini by only comparing her to living primates. You cannot use paleontology to prove a point while simultaneously ignoring all of the other paleontological finds.

The autism-vaccine crap utilized something else entirely, several somethings to be more precise. It relied on a small uncontrolled study (12 data points) to draw sweeping conclusions. Data were manipulated to show a stronger correlation. Some of the children had medically documented problems BEFORE they received the vaccines while others did not show any problems even after being vaccinated (except in the paper). So these data were very well cooked and manipulated to fit the conclusions Wakefield (and/or the lawyers that had been paying him) wanted.

The arsenic DNA debacle is the most recent of these cases of highly publicized bad science. If you look closely enough, though, you can find a number of similarities between the “science” of all of them.

1) There’s always a press conference in really bad science, not like “MHC effects mate selection” bad–which was pretty bad, but seems to be an honest mistake, but “not even wrong” bad or ignoring/misrepresenting previous research.
2) The paper is always released at the same time as said press conference leaving no time for review.
3) The data/methods/conflicts of interest are not fully disclosed

There are a few other things that these cases have in common:
1) Discrepancies between the press conference and paper
2) Overly simple explanations of the paper during the press conference
3) The press conference will often present wild implications of the scientific impact of the paper.

If all of these high profile press conferences continue to be facepalm inducing botches, it will continue to diminish the public perception of science. So, as someone educated but (unfortunately and not by choice) not active in the scientific community, go where the research leads, not where you want the data to lead.

Randall Munroe does it again

Ok, so Arsenic-based-life isn’t exactly what I would call it, it’s just a really neat extremophile. And while extremophiles are pretty awesome little beasties for illustrating the conditions life as we know it can survive, it doesn’t exactly live up to the hype like another recent find. It particularly pisses me off when a press conference is held at the same time and on the same day that electronic versions of the paper are released and before anyone can accurately provide dissenting opinions and critiques of an overhyped paper. Give a few leading scientists that also happen to be writers (Switek, Myers, Smith, Laden, etc.). Don’t just slam a factually unprepared press with crap for them to imbibe like dehydrated camels, let alone not release the methods or data in the press conference. It’s in the paper behind a pay wall (which I shelled out for in this instance, although in retrospect, I shouldn’t have). I have a feeling any hyped up press conference won’t be getting any attention; they don’t merit it.

Until we find entropy-defying chemical systems on another planet, the term Astrobiology should be limited to philosophy.

Genetics and Stupidity: Part 1/307000000

Those of you familiar with the actual genetics of genetically modified foods would probably laugh in the face of those in opposition to the latest spat with transgenic salmon. What they did was change the promoter sequence for one of the regulated growth hormones for one that is always expressed. In order to do that, they took the growth hormone from Oncorhynchus tshawytscha and used the promoter for an antifreeze gene found in Zoarces americanus and fused the two. This was then integrated into the genomes of Salmo salar to produce breeding stock. After generating a breeding population of homozygous fish, females were then exposed to a hormone which causes the fish to generate male gonads. So you’re left with genetically female but physiologically male fish capable of fertilizing wild-type eggs to produce a homogeneous brood of heterozygous females. Since most people don’t really care about the environmental health, and are only concerned about their own tiny worlds, I have decided to only glance over the ecological dangers (which do exist, and are fairly well dealt, although not to the extent I would like) and focus instead on what health risks such modifications carry.

Growth hormone levels are typically regulated by a myriad of factors ranging from time (time of day, day of year, and years of age) to food intake to environmental cues (such as dietary changes or, as in the case with Salmon, re-exposure to fresh water). The change here is in the sensitivity of the promoter, keeping the “time of day/day of the year” parts of the promoter sequence in the “on” position while diet and food intake still influence total growth hormone levels. The only real change here is that the gene is on for longer, but not in higher levels. This means that consumed genetically modified salmon have no instantaneous higher levels of these hormones than do wild salmon, they just have the highest levels seen in wild salmon more frequently (although, in simulated wild conditions, the fish isn’t much larger; 3-5%). The difference is seen in saturation diets where this fish is fed at maximum rates. These conditions (as would be present in fish farms) produce markedly larger fish (30-50%). This means more food, at lower cost per unit weight, than would be attainable by wild-type salmon.

As for the ecological issues, as previously mentioned, the very slight size difference under wild conditions, in conjunction with >97% sterility, enclosed facilities, and the high predation rate of salmon means the risk of genetic contamination is fairly low (although I still think a synthesis gene for an easily supplemented nutrient of some kind should be employed) for wild stock.

Part 2 of this will examine what foods are genetically modified…

Four Loko Fiasco

I sometimes wonder how often people stop to consider how full of shit they actually are. Let’s actually think about this a bit, we’ll start with one of my personal favorite drinks.

Red Bull/Vodka=quite tasty, but it is 16% alcohol with 80 mg caffeine per 14.3 oz

In other words, it has a higher content of alcohol but probably lower content of caffeine when compared to this Four Loko drink. Since the quantity of caffeine actually in this beverage isn’t disclosed and I don’t have access to an HPLC (if you do, have a caffeine standard, and feel like running a few dozen samples, let me know!) then I can’t compare the two accurately. For comparison, most energy drinks in 23 oz cans contain 160 to 200 mg of caffeine, but we’ll up it to the concentration found in Red Bull, so a total of 240 mg of caffeine. If (this is probably an overestimation of the level of caffeine) you consider the alcoholic content and caffeine ratios between Red Bull/vodka and hypothetical Four Loko you get something like this:

Red Bull/Vodka: .16 oz of alcohol and 5.6 mg caffeine per oz

Four Loko: .12 oz of alcohol and 10.4 mg caffeine per oz

I would like to point out to everyone out there that 240 mg of caffeine is already dangerously close to caffeine intoxication conditions, so we shall assume the company wasn’t completely stupid and instead adopted a lower “yield” of about 160 mg. Now, are the makers of this drink stupid enough to put the higher,  dangerous, concentration of caffeine into their drinks? I certainly hope not. The alcohol in one drink, while significant, would elevate the BAC to about .11 for a 200 lb individual if drank rapidly (Δt=0). For comparison, that is the equivalent of a four decent beers. Have two of these, and you’re looking at a little over a six pack and definite caffeine intoxication.

While Four Loko may, in fact, be dangerous, the danger comes more from irresponsible drinking and caffeine intake than from any particular beverage. Let us examine who is being hospitalized for drinking this:

“Four Teens Hospitalized”
“Denton police say drunken boy’s crash killed his girlfriend; both were 14”
“Sgt. Ed Wessing tells The Arizona Republic 18-year-old Lanae Cummins of Mesa told police she was playing the drinking game at a friend’s house”

Holy hell, every single one of these is under the legal drinking age? Perhaps better enforcement of the laws already on the books would be useful? Let’s keep going.

“Troy officers arrested two 18-year-old males around 1:40 a.m. Tuesday morning on New King Drive after seeing the vehicle they were in speeding. The vehicle exited from Northbound Interstate 75, south of Long Lake Road, according to police.
The men said they were traveling to Oakland University.
The officer searched the vehicle and said he confiscated twenty-four 12 oz cans of beer, six 23.5 oz cans of Four Loko and a single 1.75 liter bottle of vodka.”

“Standing with the grandmother of a 18-year-old Long Island girl who died after drinking Four Loko, the Democratic senator said federal and state regulators have already wasted too much time studying the issue and must move to ban sales of the beverages.”

Do I really need to fucking continue? Don’t ban something because you can’t enforce the laws already on the books. I’m interested in the FDA’s actual findings and research and look forward to reading it, but for fuck’s sake people, quit blaming the manufacturer for the failures of the parents and already existing alcohol regulations.

The Origin of Life: Storytelling or Science?

The events and narratives which follow are mostly fictional. Those parts in bold are historical fiction while those in italics are mostly speculation. Sections which lack any embellishment are my explanations and descriptions.

We shall start from a few billion years after the beginning of time, so not the very beginning, but before anything we would call living (at least on this normal little planet orbiting a normal little start in a relatively quite part of a normal galaxy in a mostly empty portion of the universe). We begin when the planet has cooled enough to sustain standing water on the surface. When was this? Some time between 4.4 and 4.2 billion years ago. Approximately two hundred million years after the collapse of the nebula which formed the Sun. The oldest known fossils date to approximately 3.5 billion years ago. This is where our fictional narrative ends, and it shall be denoted as T=0, for dating purposes, we’ll pretend it is PRECISELY 3.5 billion years ago. This is not to say there is no evidence of biological activity before this time, since the oldest evidence for biological activity (in the form of biochemical markers of biological activity) date to 3.85 billion years ago.

What Biogeography Tells Us

Lots of things can be learned from biogeography. Far more than just what species live where. The evolutionary relationship of animals combined with our knowledge of biogeography can assemble a rather interesting interesting map of relationships. Before genetics was well established, biogeography played a large role in determining the relationships of extant closely related species (often not beyond the terrestrially bound kinds) such as reptiles, amphibians, and (excluding Chiroptera and Cetacea) mammals when morphology did not provide enough information, such as the Agkistrodons you should be familiar with by now, if you’ve read my blog at all. Interestingly, genetics alone does not precisely tell us about a fascinating little subspecies/species/whatever the hell taxonomists decide to call it known as Taylor’s cantil (A. bilineatus taylori/A. taylori). It is certainly a species in the sense of the Biological Species Concept (Mayr) and the Cohesion Species concepts (Hull) but not the Ecological Niche Concept (Simpson). More interestingly, where exactly this population fits within the Agkistrodon genus is not fully shown by the genetic data. This is because it appears to be a near-simultaneous three-way split between the subspecies/species of the A. bilineatus group (including A. taylori) and the A. piscivorus group. The Gulf Arc hypothesis postulates that a single interbreeding population of the ancestral A. bilineatus/piscivorus existed around the entire Gulf of Mexico and up the Pacific coast of Central American and Mexico (pretty much it’s present range if you fill in the gaps) and something caused gaps to form in the populations at (very slightly) different times resulting in species that are genetically as dissimilar to each other as they are to any other within the group, but also isolating them and further enhancing all of the distinguishing features which existed among each subpopulation within the entire Gulf Arc. What we know about the changing geography shows the formation of new features which could have resulted in the relatively recent speciation.

It requires both the genetic and geographical information to conclude such a model (genetics alone without any knowledge of the geography (or morphology, ecology, and behavior) would only be capable of indicating A. taylori is a reproductively distinct species from A. bilineatus and A. piscivorus and would be incapable (because of how recent this event was) of demonstrating when this occurred.

On the engineering of organisms, or unintelligent design

I’ve been recently confounded by the “argument from remarkable engineering” fallacy against evolution. It is, quite frankly, only puzzling because it is still in use. The Behe-esque argument was made regarding human development and how remarkably elegant and complicated it was, therefor god. Allow me, for a moment, the chance to slam a lid on embryonic development as an example of remarkable engineering.

If you’re like me and just love learning about embryology beyond the point most people would consider sane, I have a few resources for you. It was brought to my attention-yet again-that I can be a bit masochistic when it comes to learning, so I’ll spare you the long list of “shit that breaks” in the genome. If you’ve ever tried to disassemble a lawnmower engine before you were 10 years old, you might find this wikipedia entry as interesting as I did, but since most people won’t or haven’t, I’ll skip it; it’s also just a list of the disorders and associated mutations. It doesn’t break down all the different types since, honestly, there are dozens of specific mutations for any one disorder and it also leaves out quite a few. I kind of wish it also listed the allelic variations as well, but I can’t have everything, now can I?

How can things go wrong in the development of an embryo? Well, you have 6 basic “types” of errors ranging from the not-so-serious to the abortion-inducing (note: I mean spontaneous abortion, not “have an abortion because it will have three eyes, no legs, and be hermaphroditic”–although that is also possible).

1. Polyploidy (extra copies of chromosomes; I include monosomies here, too)
2. Mutations (changes in the actual DNA sequence)
3. Exposure (to either environmental signals or toxins)
4. Unactivated/deactivated pathways (caused by external or internal interference or mutation)
5. Overexpression (see  explanation of #4)
6. Physical trauma (lethal–for the embryo/fetus–oxygen/nutrient deprivation)

To be human is to lack all of the terminating errors and be left only with non-lethal ones. We all have new mutations which our parents did not have; every single one of us has multiple new mutations which could be among any type of mutation: duplications, deletions, frame-shifts, mismatches, etc. Some of us even have trisomies (which are typically lethal) and monosomies (which can be lethal).

The first of these includes Down syndrome (trisomy 21), Trisomy-22, Edwards syndrome (trisomy 18), Patau syndrome (trisomy 13), and pretty much one for every chromosome, although many (including Patau syndrome) result in miscarriage. For survival of the embryo with one of these trisomies which often result in miscarriage requires genetic chimerism where the founder cells are two fertilized ova rather than only one–this can result in non-identical twins or a single chimera. Chimeric individuals can survive with a trisomy which would normally result in death since the other cell line is capable of “filling the gaps” where the trisomy-containing cells could not, such as in many functions of the kidneys or heart or liver (depending upon the trisomy). None of these, I would say, are marvels of engineering.

As mentioned previously, every last one of us has a mutation of some kind, so to say that “human” is a specific genotype with no variation is to miss the point entirely.

[tangent] The “human genome project” was actually an “average human genome project” which did nothing to elucidate the subtleties and complications involved. An example of a complication is the following: hypothetically, an individual can have the mutation for sickle cell anemia, but if another mutation exists (such as an increase in α₂γ₂ hemoglobin production as opposed to α₂β₂), then the person develops (almost) normally. Almost because the γ subunit gives a slightly higher oxygen affinity than the β subunit. This is essential due to fetal blood needing to “steal” oxygen from the maternal blood supply.[/tangent]

We are, above all, products of a procedural development, and as new types of cells arise procedurally, they influence the development of additional ones through the same processes of feedback. Procedural development, as a bottom-up process, is inherently unstable and easily broken. How easily? Consider that the removal of a specific single molecule at the beginning of an open reading frame can result in the lack of an entire protein or multiple proteins (if the initial one is a promoter or enhancer or regulatory protein, it could be hundreds). If this (these) protein (s) is/are necessary for survival of that particular cell line or used in a (or many) vital process(es),not all are, then the cell or organism will die. Is this a good design?

The mutations which do arise in all organisms result in evolution, but evolution is, for lack of a better phrase, all about mistakes. These mutations which an organism can live with (and reproduce) are those that rise to higher frequency within the breeding population.

There is an illusion of design resulting from non-lethal mutations being selected AGAINST, not for. Those alleles which confer relative advantage result in decreased success of other alleles in the same population. The previous sentence is VERY important. If a population is isolated, only the alleles present in that population will be subject to any selective pressure unique to that population.

Since mutations arise randomly, and genetic drift “noise” can further complicate the evolutionary history of an organism. The end results of these processes may look, on the outside, to be finely engineered organisms, but the deeper one delves into the anatomy and genetics of an organism, the more of a mess it becomes.

Way too busy

Ok, so I can finally start doing a bit of blagging again. I have a few photos to share, but first, it’s a mysterious mystery.

Can you find this guy?

He’s hiding somewhere in this image:

You’ll probably have to view the image full size…

I found him just before I went to cut grass.

Raining oil?

It’s certainly possible youtube user HistoryTours is correct in saying Louisiana experienced oil rain. If you listen to television and news meteorologists, oil doesn’t evaporate, but this certainly isn’t correct. The boiling point of light oils (pentane and lighter) is below the current temperature of the Gulf of Mexico. It is possible that this fell along with the water which evaporated from the same area. Below are several of the videos which he uploaded. I have requested additional information from him and hope to keep everyone up to date.It is definitely in the New Orleans area. Thanks to Stacy for the pointer.

Want a miracle?

Then get off your fucking knees and grab a shovel, donate some money, wash some birds, or even just buy a candle.

Quit praying and do something.

/rant