Scientists behaving deviously

Cas9

There are some scientific technologies that rapidly become ubiquitious and indispensible, and they become the engine that drives tremendous amounts of research, win Nobel prizes, and are eventually taken for granted. Polymerase chain reaction (PCR) is one example: PCR is routine in molecular biology now, but I remember when PCR machines were magical objects of reverence, and you were cutting edge when you used one. No more; I actually tell my senior students presenting their final thesis presentation that they don’t have to explain what PCR is anymore, everyone knows what it is and how it works and what it is used for.

The new technology of today that is going to be showered with awards and money and accolades and become totally ubiquitous is CRISPR/Cas. This technique exploits the molecular biology of a prokaryotic adaptive immune system to target gene sequences in living cells and swap in a different sequence — it’s a mechanism for going into a cell and editing its genome selectively. This is huge. It has gigantic implications — people are already fretting over the ethical use of a way to modify people’s genes, even before it has been applied in any practical way. I’m not exaggerating when I say that this is going to be the universal tool for experimental molecular biology for the next several decades, possibly indefinitely.

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But that’s not how science works!

There will be an interesting meeting in London next fall, New trends in evolutionary biology: biological, philosophical and social science perspectives. The description:

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution, although the issues involved remain hotly contested. This meeting will present these developments and arguments in a form that will encourage cross-disciplinary discussion and, in particular, involve the humanities and social sciences in order to provide further analytical perspectives and explore the social and philosophical implications.

It’s interesting because it could be enlightening, but it could also be weird and chaotic and a magnet for crackpots. Larry Moran is attending — not as a representative of the crackpot contingent, but, I suspect, to cast a cynical eye on the shenanigans. The Third Way of Evolution gang seems to be excited about the meeting, which is not a good sign — these are people who have taken some useful ideas in evolutionary theory, like epigenetics and niche construction, and turned the dial up to 11 to argue that these concepts are so revolutionary that they demand a complete upheaval of neo-Darwinian thinking.

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Friday Cephalopod: Where am I going to put a 300 gallon salt water aquarium?

This is a new one: an octopus farm. Kanaloa Octopus Farm is open for business — for $200, you can get your very own pet octopus.

octopus_cyanea

Unfortunately, they’re caught in a chicken-and-egg problem. You should not encourage the capture of cephalopods in the wild, so it’s a great idea to have a breeding program to provide animals for aquarists. But they’re still in the process of building up their stocks, so they’re selling their smaller wild-caught octopuses, which isn’t so good.

Need I point out that you also should not buy an octopus unless you have the facilities and experience to care for them properly? I have a bit of experience with fresh-water aquarium management, which counts for diddly for raising marine species; keeping cephalopods happy also requires a lot of space and a large volume of clean salt water.

This is not like that time you won a goldfish at the arcade at the county fair when you were a kid, and you plunked it into a bowl of tap water and found it dead the next day. Well, actually, it’s a lot like that last phrase.

Why a “moonshot to cure cancer” is doomed to failure

A few days ago, David Bowie died of cancer. This morning I learned that the actor Alan Rickman has died of cancer. You all know the rule of threes, right? It has been satisfied, because in his state of the union address Barack Obama announced that he was going to kill American biological research, with cancer. OK, maybe that’s a little strong: he was more devious about it. He announced a “moonshot” to cure cancer. It’s the same thing.

US President Barack Obama isn’t going quietly. He began his final year in office by announcing a “moonshot” to cure cancer in his State of the Union address to Congress on 12 January.

The effort will be led by vice-president Joe Biden, whose son Beau died of brain cancer last year.

“For the loved ones we’ve all lost, for the family we can still save, let’s make America the country that cures cancer once and for all,” Obama said in a soaring speech that otherwise offered few new proposals. Instead, the president spent most of the address looking back at his accomplishments over roughly seven years in office.

It’s not the “cancer” part of the proposal that is bad; it’s a terrible disease, and we should more to combat it. It’s two other words: “moonshot” and “cure”.

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That’s not a thesis, it’s a junkheap

pile-of-trash

Well, cool. You can download Judy Wilyman’s anti-vaccination thesis from the University of Wollongong and read it yourself. So click, click, wait a second, and…

YAAAARGH! My eyes! I thought the social sciences side of the academic world would possibly have higher standards for writing than the science side, but no…it’s awful. This should have been shredded, and Wilyman told to go back and start all over.

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My last post on Perry Marshall

Once more unto the breach in Perry Marshall’s cranium, dear friends. He is once again trying to claim that he alone has the one true understanding of Barbara McClintock’s work, and he keeps getting it wrong. It’s just embarrassing to watch.

He makes obvious statements like this:

Damage is random. Repair is not.

Well, duh. If the cell were to just go charging in and practice excision repair (a process that snips out a short piece of one strand of DNA and brings in polymerase to re-synthesize it) on random stretches of DNA, it would increase the frequency of errors. Polymerase proofreads as it goes; it checks to see if the nucleotide it just copied into a new strand properly complements the nucleotide on the other strand, and if it doesn’t, it steps back, cuts out the error, and tries again. It doesn’t repeat if they match.

This is familiar stuff. Students in our classes here at UMM get all this kind of material, in far greater detail, by their second year here. The problem is that Marshall carries it too far: he assumes that the cell “knows” the nature of the specific error made, and intelligently acts to directly repair it. It doesn’t. The cell can invoke general mechanisms to attempt repair, but it doesn’t in any way “know” what to do.

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Everything existing in the universe is the fruit of chance and necessity

barn

I’ve been informed that I’ve been at war for a while. I was surprised. Apparently, Perry Marshall thinks he’s been firing salvo after salvo at me…I just hadn’t noticed.

Oh, OK. I would just ignore him, but he’s presenting some fascinatingly common misconceptions. One of his boogeymen is chance, and I’ve noticed that a lot of people hate the idea of chance. Uncle Fred got hit by lightning? He must have done something very bad. It can’t just have been an accident. There are no accidents!

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Friday Cephalopod: Baby done growed up

Don’t you just love those photo series of the young’uns at different ages?

Developmental staging of Octopus bimaculoides. a Whole egg photomicrograph illustrates the egg stalk and the animal pole (asterisk) where the embryonic body forms. Extent of epiboly in this stage (st) 8 embryo is marked with arrowheads. b End on view of a stage 8 embryo with the egg capsule and yolk removed. In dark field illumination, the organ primordia are visible as ectodermal and mesodermal thickenings. The mantle anlage (m) is central, the prospective mouth (mo) at the top of the panel is anterior, and the arm bud pairs (1–4) are arrayed peripherally. The folds of the collar (co) and the prospective funnel (fo, ff) fall at intermediate positions. c–f The growth of the organ systems by stage 10 is illustrated in end on (c), anterior (d), posterior (e) and left side (f) views. g–m The shape of the adult octopus emerges at middle (g–l) and late (m) embryonic stages. Illustrated are anterior (g and j), posterior (h and k) and left side (i and l) views of stage 13 (g–i) and stage 18 (j–l) embryos, and an anterior view of a stage 19 embryo (m). n and o Anterior views of O. bimaculoides (n) and its brain (o) at hatching (stage 20). A, anterior view; ey, eye; fun, funnel; gil, gill; L, lateral view; olf, olfactory organ; opt, optic lobe; P, posterior view; pf, funnel pouch; st, statocyst; supes, supraesophageal mass. Scale bars: 1mm (a), 500 μm (b–o)

Developmental staging of Octopus bimaculoides. a Whole egg photomicrograph illustrates the egg stalk and the animal pole (asterisk) where the embryonic body forms. Extent of epiboly in this stage (st) 8 embryo is marked with arrowheads. b End on view of a stage 8 embryo with the egg capsule and yolk removed. In dark field illumination, the organ primordia are visible as ectodermal and mesodermal thickenings. The mantle anlage (m) is central, the prospective mouth (mo) at the top of the panel is anterior, and the arm bud pairs (1–4) are arrayed peripherally. The folds of the collar (co) and the prospective funnel (fo, ff) fall at intermediate positions. c–f The growth of the organ systems by stage 10 is illustrated in end on (c), anterior (d), posterior (e) and left side (f) views. g–m The shape of the adult octopus emerges at middle (g–l) and late (m) embryonic stages. Illustrated are anterior (g and j), posterior (h and k) and left side (i and l) views of stage 13 (g–i) and stage 18 (j–l) embryos, and an anterior view of a stage 19 embryo (m). n and o Anterior views of O. bimaculoides (n) and its brain (o) at hatching (stage 20). A, anterior view; ey, eye; fun, funnel; gil, gill; L, lateral view; olf, olfactory organ; opt, optic lobe; P, posterior view; pf, funnel pouch; st, statocyst; supes, supraesophageal mass. Scale bars: 1mm (a), 500 μm (b–o)

Shigeno et al. Zoological Letters (2015) 1:26