All of zslastman's Comments + Replies

LINK: Most of EvoPsych is pseudoscience

Here's a much better article criticizing evo-psych. I think it goes a little too far in some places, and I've posted it before, but those looking for something a bit more structured and well argued would do well to start here.

Open thread, Nov. 23 - Nov. 29, 2015

Yeah it doesn't say much. For one thing I'd say it's just about all of the genes that are differentially expressed, if you look hard enough. Regardless, that doesn't tell us how many of them really matter with respect to the things we care about, how many causal factors are at work, or how difficult it will be to fix. Doesn't rule out a single silver bullet aging cure (though other things probably do)

Genosets

Yes that's the case. To get enough data we probably need lots of in vitro experiments. Remember that data is not equal to information - even really big sample sizes wouldn't be enough to resolve the combinatoric explosion. What I mean in that comment up there (I posted it before it was finished, I think) is that there are ~23k genes in the genome, so even under the absurdly simple assumption that there's only one mutation possible per gene, you have half a billion possible combinations of gene breakages, which you will never ever be able to get enough of a sample size to look at blindly.

Open thread, Oct. 12 - Oct. 18, 2015

Ha, in theory, but it looks like the guys at TeXmacs are already selling the product for free, so no dice...

0ChristianKl6yI made with my Kindle the experience that it's better than regular paper books while reading books on a smartphone isn't. Currently most mathmaticians use paper. If someone would design a mathematical editor that's better than paper, I think that could be a huge commercial success.
Open thread, Oct. 12 - Oct. 18, 2015

Yes, that would also be great, but I a) I can't afford such a tablet, and b) I strongly suspect that the OCR would be inaccurate enough that I'd end up wishing for a keyboard anyway. Hell accurate voice recognition would be better, but I'm still waiting for that to happen...

1NancyLebovitz6yNow that I think about it, OCR would be much harder for math than for text.
Open thread, Oct. 12 - Oct. 18, 2015

Been using it for an hour now,and yes, it's crashed on me once, but no more than half the other programs I use. Already seeing the benefits of it when I spent half an hour doing something, realised there was a mistake at the start, and could then just find/replace stuff instead of scrunching the paper up into a ball and cursing Pierre Laplace. Also I don't have to deal with the aesthetic trauma of viewing my own handwriting. Outstanding.

Open thread, Oct. 12 - Oct. 18, 2015

YES. Thank you so much. Texmacs seems to be exactly what I wanted.

3gjm6yExcellent! I will mention that I have occasionally had it crash on me (this was in the past, probably an older version of the software, so take it with a grain of salt -- but you might want to be slightly more paranoid about saving your work regularly than you would be with, say, a simple text editor).
Open thread, Oct. 12 - Oct. 18, 2015

pen and paper is far more instant than any method I can imagine of poking mathematics in through a keyboard.

Yeah... I think I just have to bite this bullet. If you do math professionally and the people you know work onto pen and paper, then that's the answer.

It's just.... I feel like I can imagine a system that would be better than pen and paper. There's so much tedious repetition of symbols when I do algebra on paper, and inevitably while simplifying some big integral I write something wrong, and have to scratch it out, and the whole thing becomes a c... (read more)

1NancyLebovitz6yWould it make sense to write on a tablet and have the computer do OCR? (Hypothetical system.)
0ChristianKl6yThat means there's a possible startup.
Open thread, Oct. 12 - Oct. 18, 2015

Yeah I can imagine doing that all right - I wouldn't actually mind writing in latex even, the problem is the lag. Building a latex document after each change takes time. If the latex was being built in a window next to it, in real time, (say a 1 second lag would probably be fine) there'd be no problem. I'm not looking to publish the math, I just want a thought-aid.

1tut6yI believe that there is an editor called lyx that lets you do this.
Open thread, Oct. 12 - Oct. 18, 2015

Why isn't there a good way of doing symbolic math on a computer?

I want to brush up on my probability theory. I hate using a pen and paper, I lose them, they get damaged, and my handwriting is slow and messy.

In my mind I can envisage a simple symbolic math editor with keyboard shortcuts for common symbols, that would allow you to edit nice, neat latex style equations, as easily as I can edit text. Markdown would be acceptable as long as I can see the equation in it's pretty form next to it. This doesn't seem to exist. Python based symbolic math systems, lik... (read more)

What would be really nice is tablet software that can translate handwritten math into latex, and compile that into pdf.

By the way, what I think you want is not "doing symbolic math on a computer," but "having a good input method for equations."


edit: Also can someone please write a good modern programming language for typesetting? With all due respect to Dr. Knuth, tex is awful.

8gjm6yI tend to use TeXmacs [http://www.texmacs.org/] for this. It's a WYSIWYG document editor; you can enter mathematics using (La)TeX syntax, but there are also menus and keyboard shortcuts. It's free in both senses. No symbolic-manipulation capabilities of its own, but it has some ability to connect to other things that do; I haven't tried those out. Mathematica isn't that far from what you want, I think, and it has the advantage of being able to do a lot of the symbolic manipulation for you. But, as you say, it's really expensive -- though if you haven't checked out the home and (if applicable) student editions, you should do so; they're much cheaper. Anyway, the fact that to me it sounds close to what you want makes me suspect that I'm missing or misunderstanding some of your requirements; if you could clarify how it doesn't meet your needs it may help with suggesting other options.
2RichardKennaway6yWould any of these [https://github.com/mathjax/MathJax-docs/wiki/List-of-web-based-math-editors] be useful? That's just a list I found by Googling /MathJax editor/. I'm not familiar with any of them. MathJax is a Javascript library for rendering mathematics on web pages. The mathematics is written in MathML. I use pen and paper, and switch to LaTeX when I have something I need to preserve. It's not very satisfactory, but since anything I might want to publish will have to go through LaTeX at some point, there's no point in using any other format, unless it had a LaTeX exporter. And pen and paper is far more instant than any method I can imagine of poking mathematics in through a keyboard.
1MrMind6yI don't know either of a program that solves your problem. But writing a transcompiler from mathematical markdown (mathdown?) to Latex should not be that difficult in F#. It should be a fun excercise, if you write the formal grammar.
Why people want to die

I'm always puzzled by how many how many LWers seem to casually dismiss the reality of mortality with appeals to singularities, cryonics etc. I'm sure immortality is coming, but I don't see much chance of me living to see it. Seems prudent to come to terms with that.

How to win the World Food Prize

See my answer on the other thread :) Difficult to estimate. You need a new method of transgenesis - 5-20 years?

Genosets

Hmmmm. I'm shamefully ignorant about prices, but I would estimate such an effort would be in the tens of millions, if you wanted it done quickly (and it will still take a while). As far as I'm aware we haven't developed methods for transgenesis in Tetse flies, having only gotten the genome sequenced in 2014 (priorities people?!), and setting it up in a new organism in a new organism with an unusual life cycle can be surprisingly difficult. The link below describes techniques for manipulating gut microbes in the flies, which I don't think would suffice.

In ... (read more)

0dapc4yI really appreciate the explanations in this thread. I was wondering if anyone had an update regarding recent developments in this space. Specifically, using big data to solve for genetic / protein links to phenotypes. I have also been struggling to find more recent information regarding genosets. Apologies if any of that is unclear, I am still relatively new to this.
How to win the World Food Prize

I'm totally in favor of chlorinating that pool, but just bear in mind that the 'registry of standard parts', and other biological tools in general, like CRISPR, are nowwhere near as easy to use and reliable as it says on the packaging. I'm always amused by the contrast between articles about CRISPR which make it sound like you can just jam a thumbdrive into a mouse, and the people I know trying to get CRISPR to work on a new cell line or organism, who are up all night for months in a row muttering schizophrenically in the cell culture room. You need a lot of time and human capitol for these things.

0[anonymous]6yBased on your more intimate knowledge and access to knowledge in the area, what kind of time frame (even an order of magnitude estimate would suffice, if the former is intractable) would we be looking at if an amount of resources, proportional to the potential humanitarian impact relative to mosquito transmitted diseases, where to be spent to develop a gene drive ready for use in the Tsetse fly [https://www.wikipedia.org/wiki/Tsetse_fly], a species regarded as responsible for preventing an African 'green revolution' [http://www.givewell.org/international/economic-empowerment/agriculture] like was seen in Asia and thus part of the whole fable of African starvation? Any way to incorporate resource investment into mitigating relevant risks? [http://www.files.givewell.org/files/conversations/Kevin_Esvelt_3-31-15_%28public%29.pdf] . It seems like an academic has independently started thinking along the same lines [http://www.ncbi.nlm.nih.gov/pubmed/12878419].
Genosets

Another genomics PhD here. It's a complex topic. We know that combinatorial effects (epistasis in genetics lingo) matter, from population genetics studies in model organisms. This is despite the fact that simple linear models perform well in the human population - provided they are against some reasonably constant genetic background, low allele frequencies mean that the combinatorial effects are well captured by linear ones.

The problem is that even if you only care about pairwise combinations, there are far too many of them, given a uniform prior. Even if ... (read more)

0[anonymous]6yOP here. Having learned more statistics since I last posted - I reckon it could be as simple as exploring various interactions (effect modifications) in the data with respect to additional SNP's. The issue would be that interactions require greater sample sizes to avoid spurious results and most genetics research has woefully low sample sizes which would only be harder to overcome when inching towards more personalised medicine based on individual genomes.
0[anonymous]6yBased on your more intimate knowledge and access to knowledge in the area, what kind of $USD investment (even an order of magnitude estimate would suffice, if the former is intractable) would we be looking at if an amount of resources, proportional to the potential humanitarian impact relative to mosquito transmitted diseases, where to be spent to develop a gene drive ready for use in the Tsetse fly [https://www.wikipedia.org/wiki/Tsetse_fly], a species regarded as responsible for preventing an African 'green revolution' [http://www.givewell.org/international/economic-empowerment/agriculture] like was seen in Asia and thus part of the whole fable of African starvation? Any way to incorporate resource investment into mitigating relevant risks? [http://www.files.givewell.org/files/conversations/Kevin_Esvelt_3-31-15_%28public%29.pdf] . It seems like an academic has independently started thinking along the same lines [http://www.ncbi.nlm.nih.gov/pubmed/12878419].
When does heritable low fitness need to be explained?

Short answer - no, this is a hard, ongoing problem.

I think you're looking for the concept of 'mutational variance'. This is the amount of variation in a trait that is generated by random mutation. The variance in a trait is going to be determined by the balance of mutational variance and selective effects. Things with lots of genes effecting them will have a large 'mutational target size'. So for instance intellectual disability has a large mutational target size because there are so many different ways to break a brain, while some kinds of haemophilia hav... (read more)

Whole genome sequencing vs SNP genotyping

WGS is going to get cheaper and cheaper as time goes on, presumably in the future we'll have developed a process for analysing the results properly. In the intervening time, there isn't much to be gained from it. SNP genotyping gives you most of the info about common variants, because the things it doesn't catch (deletions, insertions, etc.) will generally have some SNP in linkage to them. The rare variants are what you miss, and right now we don't really know what to do with them.

In general I wouldn't overestimate how much genotyping will tell you. Your family history is likely to be more informative.

Request for Advice : A.I. - can I make myself useful?

I should be clearer on that score. It's not that I see a high likelihood of a singularity happening in the next 50 years, with Skynet waltzing in and solving everything. Rather I see new methods in Biology happening that render what I'm doing irrelevant, and my training not very useful. An example: lots of people in the 90s spent their entire PhDs sequencing single genes by hand. I feel like what I'm doing is the equivalent.

Request for Advice : A.I. - can I make myself useful?

Cognitive genomics is definitely something I"ll look into, thanks.

0RyanCarey7yYeah, cognitive genomics could help humans to be smarter when we have to deal with an AI. It could have bad consequences too, mind. There are only some dozens of people who have the guts to work directly on the problem of cognitive genomics, so if you got in this field, you wouldn't have to worry that your research was pointless. Rather, you could become a useful point of contact for people thinking about future tech. Here are a couple of relevant articles. https://intelligence.org/2013/08/31/stephen-hsu-on-cognitive-genomics/ [https://intelligence.org/2013/08/31/stephen-hsu-on-cognitive-genomics/] http://arxiv.org/pdf/1408.3421.pdf [http://arxiv.org/pdf/1408.3421.pdf]
Request for Advice : A.I. - can I make myself useful?

Thank you, I'd never heard of Emerald Cloudlab. I guess I was speaking too much from my own observations and without enough research.

0ChristianKl7yThe fact that you can do your PHD without being aware where real innovation is happening is a good illustration of the poor state of academic biology. I don't think there are easy solutions for fixing academic biology, but it's an important problem. The key is to step up a meta level. It might be harder to get grants to work on that level but the possible gain is much higher. In some sense the biosafety issues are also up one meta level. I think the Cloud approach is here really great. In a laboratory you can do things implicitly. In a cloud experiment you have to specify everything explicitly. Emerald Cloudlab allows free hosting of all the experimental data if a researcher makes the data publically available.
Request for Advice : A.I. - can I make myself useful?

I don't mean to come across as super optimistic with respect to strong A.I., or even A.I. in general. I should have written '50 years give or take 50'. It's just that i think my field's progress rate is determined by the inflow of methods from other fields, and that the current problems it faces are insoluble using current ones. I think people who aren't immersed in the field get a mistaken impression about this because papers and press releases must communicate an artificial sense of progress and certainty to succeed. Word in the trenches is that we're mi... (read more)

Request for Advice : A.I. - can I make myself useful?

This all hits the nail on the head I think. The marginal value of my PhD is, I'm convinced, at most zero, and perhaps negative, because it adds to the noise. The replicability of papers is significantly hindered by lack of automation, to my mind.

Also, saying that we don't know what 1/4 to 1/3 of human genes do is wildly optimistic. Better to say we have some idea what 2/3 of them do.

Request for Advice : A.I. - can I make myself useful?

I have. I'm not wholly decided but as far as I can see the field suffers from most of the same problems that other biological fields do, and is also a bit overcrowded - research funding is pouring into it lately, and I think you could do more good by researching other fields that would feed them better methods, than by working in it directly.

Request for Advice : A.I. - can I make myself useful?

I'd much rather learn C++ for all it's faults, since it meshes so nicely with R and Python, but people keep telling me to learn Java...

What I"m referring to in my field specifically is understanding gene regulatory networks. I've become convinced that the only way we're going to get a hold on them is by actually simulating the biochemistry. Searching for higher level abstractions within them just doesn't work that well. This will require lots and lots of experiments, which are currently done by hand, to be automated, and the results to be synthesized ... (read more)

Request for Advice : A.I. - can I make myself useful?

Yes. I'm rather annoyed at myself for only now giving level 3 the kind of attention it deserves. Level 3 is hard though. Largely because other people can't help you as much. I'm kind of agnostic about what I want, to be honest. Nor do I have good information about my comparative advantages (due to relative ignorance of other fields) and the magnitudes of the trade offs to be made. Now is a time when I can take the time to think on and research these questions.

I'd estimate my altruism fluctuates between zero and ~70% on a daily basis, with a peak in the mornings immediately after get caffeinated.

2adamzerner7yYou're fortunate - that's the sound rationalists make when they level up [http://lesswrong.com/lw/ul/my_bayesian_enlightenment/] :)
Request for Advice : A.I. - can I make myself useful?

These are all good points. And you're right that A.I. and robotics will come (for a while presumably) in the form of incremental improvements, as they already are.

I guess it feels to me though, like the rate of improvement is basically independent of biology itself, and is determined by the rate at which other fields hand it technology. Sequencing being a good example. We've basically done it to death now, and are waiting for someone to give us better methods that will yield new insights. The major bottleneck at the moment is that we insist on using grad s... (read more)

2ChristianKl7yThat's not true. Peter Thiel's Founders Fund for example backs http://emeraldcloudlab.com/ [http://emeraldcloudlab.com/] which automate basic laboratory tasks. They seem to have enough customers to have a waiting list. I don't see a "Jobs" page on their homepage at first glance, but I would expect that they are a company that can make use of your skills. It might very well be possible to get a meaningful happiness score out of high resolution GSR data and heart rate data. A few years ago I heard that they manage to do emotional detection with 80% accuracy. Having an objective way to measure happiness on a daily basis would be huge for treating depression and measuring which drug works. Today's heart rate monitors might not be high accuracy enough, so there's a need to provide applications for higher resolution monitoring to incentivise Apple, Samsung and Microsoft to develop the tech for smartwatches. GSR data is very useless if you don't have an algorithm interpreting it but once you interpret it you can pick up bodily events. Besides developing the actual hardware developing statistics like that, that provide meaningful insights seems to be important to me. Developing better scales for obesity isn't only about producing new technology but also about analysis of data. The fact that we have an open access uniprot is also not just about technology. If you look at chemistry where the American Chemical Association claims ownership of CAS numbers, the state of affairs is worse. Thinking about getting more knowledge into a format like uniprot, isn't just about technology but requires thinking about ontology. I like Barry Smiths work in that area.
Request for Advice : A.I. - can I make myself useful?

Research (that I've seen) is in general patchy and inconsistent. But I take your point, it might be a frustrating enterprise. I think concentrating on a specific area is almost certainly a good idea.

Request for Advice : A.I. - can I make myself useful?

This is the kind of 'I-wouldn't-have-thought-of-that' answer I was hoping for.

It would require substantial retraining, but this seems like a direction I could move in by choosing the appropriate post-doc, while also doing some useful work along the way. The general class of 'using biology to ensure the future occurs' contains a lot of potentially interesting things like plant biology and research involving things like salt and pathogen tolerant crops. Looks like I have some research to do :)

0[anonymous]7yDid you, by any chance, read Andre Almeida on trehalose and desiccation/salt/cold tolerance in plants? (Not that that's particularly interesting, but my impression was that it was 'solid'.) (Also, sometimes people develop salt-tolerant wheat in vitro without any research as to how its symbionts in vivo influence its performance, which should impact study reproducibility.)
Open Thread, May 4 - May 10, 2015

Jayman is correct that adoption studies typically show negligible parental effects. But remember the studies can only talk about the environmental variation present in their data, and are generally done on normal, western, middle class cohorts. In studies where they include stronger environmental variation - e.g. Turkheimer et al 2003, you find that it matters.

So basically, the kind of parenting choices that people typically worry about are probably meaningless, but severe trauma, poverty, abuse etc. do matter. That being said, You can't just say "X is difficult to encapsulate" with studies. This is a fully general counter argument to any evidence you don't like.

-2SanguineEmpiricist7yThat's not what I'm saying. I'm just saying that even if a small percentage of the population took that advice as definitive and executed over it, all latent small probabilities would be realized and the mistakes would be immediately manifested. Stuff like that isn't being difficult as any pharmaceutical company or any medical company has to know for sure that their studies/devices are correct for health effects. In fact in statistical decision theory texts pharmaceutical examples are standard. tl;dr this would be a big lawsuit of some sorts
My third-of-life crisis

I'm a non-smoking vegetarian teetotaler who has to walk a kilometer between home and the bus stop. I hope that >counts.

Actually, in my experience, the amount of exercise needed for strong benefits to mood and energy is about 20 minutes hard exercise (talking during becomes difficult), at least 4 days per week. You could take up running. Murakami swears by it.

I don't have any suggestions for solving that, but I do think that as long as you hold that conflict it's going to be a big >obstacle to moving in any direction.

This. It may help to see yo... (read more)

My third-of-life crisis

Much sympathy. Your chosen career is a risky one and there probably isn't a way to make it safe - otherwise there would be even more writers than there are now. The way to avoid years of dread seems to me to have a good side job, one that leaves you with some energy to write. Some thoughts:

1) You may want to think about how you can overcome your disgust with all things economic - your parents poisoned that aspect of intellectual life, but economics is fairly well regarded here abouts - maybe you can salvage it for yourself by making it your own? Coming at ... (read more)

4polymathwannabe7yI will acknowledge there's a huge component of pride in this. I don't want to give my family an opportunity to tell me they were right in their choices all along. When I joined the publishing company after three years in various call centers, my brother described it as "finally seeing sense." You've no idea how much I envy backpackers, but the prospect of not having a secure paycheck terrifies me. I live cheaply already; it's just that I let previous roommates leech off me for too long and I'm still catching up with the effects of my misguided helpfulness. Indeed, enough stuff for a thirty-season soap opera. But that's not the kind of stories I'm interested in exploring, at least not too overtly. My story ideas have other questions to answer. I can write. I may never get published. I need to figure out how to use the former to fix the latter. True, I'm not getting enough sleep these days, which should be fixed next month after I deliver a huge assignment at the office and my final exams for this semester. I'm a non-smoking vegetarian teetotaler who has to walk a kilometer between home and the bus stop. I hope that counts. [edited to fix spelling]
Academic papers

"I didn't have time to write you a short letter, so I wrote you a long one" I think the rapid part is in terms of the writer's time, not the readers'.

0[anonymous]7yI didn't mean the readers' time: probably in average it takes me less to read an academic paper than to read a Slate Star Codex post, at least if the latter is tagged as “long post is long”. :-)
2[anonymous]7yDo you have an idea how long it takes to write and publish a paper in a peer-reviewed journal?
0ChristianKl7yIn a world of publish or perish and a lot of articles getting rejected I don't thing the problem is that researchers don't invest enough time in writing papers. It's rather that there are incentives for writing in a way that signals sophistication. Peer review also adds extra time for the communication process.
Stupid Questions (10/27/2014)

Yes, ignoring this advice was in retrospect very foolish. I badly underestimated how important the supervisor/student relationship is. I'm going to be a lot more careful next time.

Stupid Questions (10/27/2014)

Teaching is something I would love to do, but I was given to understand that you basically have to do research nowadays, due to the glut of academics.

1James_Miller7yIt depends on the field and the school. If you don't care about status, you will have a much easier time finding an academic job where teaching undergrads is considered an important part of your job.
Stupid Questions (10/27/2014)

There are a lot of things wrong, I don't know which of them is the most important...

1)I have zero control over my own work. I am working frantically all the time to complete analyses requested by other people, most of which turn out to be useless or ill thought out. People generally don't understand programming and stats enough to know how long things should take.

2)My boss is widely regarded as a bit of a tyrant. I have a powerful aversion to interacting with her in any way, and she has extremely poor communication skills. Our relationship is terrible. I t... (read more)

1Gunnar_Zarncke7yIf you need a plan to improve your situation you might consider Athol Kay [http://marriedmansexlife.com/the-mindful-attraction-plan/] for advice. He is not uncontroversial (see this thread [http://lesswrong.com/lw/i0b/open_thread_july_1622_2013/9e8j]), but he provides you with a clear tested plan to deal with your situation (the book is not only about person-relationships but also written if you are attached to a job).
9chaosmage7yGet in touch with them. They'll understand your frustration, and might sympathize enough to give you better help than we can.
Stupid Questions (10/27/2014)

I'm a year from completing a PhD in genomic science. I am now completely disillusioned with my field, and indeed professional life in general. I entered with ambition, and have been cleansed of it. I didn't quit early on because I lost all my self esteem and assumed the problem lay with me, and that I would be equally unhappy elsewhere. I'm now almost sure this is wrong, but I only have about a year to go, and no idea what to do next, and am fairly well paid, so quitting seems imprudent.

I have basic statistical and coding skills (whose usefullness in the r... (read more)

5BarbaraB7yA response from someone, who is happy in research of biosciences: The personality of your boss is very important. I always payed a lot of attention to my emotional responses to potential bosses during interviews. Privately asking for the opinions of their subordinates can also help. As you write below, your boss "is widely regarded as a bit of a tyrant". There must be a way to find out in advance next time. For me, the meaningful topic is not enough to save the job, if the boss is a toxic person. On the other hand, the less sexy topic can become meaningful, if the boss lets you follow your curiosity and your ideas (within the constraints of the budget). The working hours are also boss-dependent. However, I must make one point - I am not saving the world or hitting for the Nobel price. My goal is to play and be somewhat useful to society while doing that. None of my papers is a dramatic thing, it rather feels like a tiny drop into the ocean of knowledge. Some people at lesswrong say: if you do not perceive your topic as the most important issue of the world, change the topic. This is the test I would not pass. I just hope to be a little helpful.
1James_Miller7yI don't know what the academic job market is like in genomic science, but if you would take pleasure in teaching you might enjoy working at a liberal arts college, which would likely be a very different environment then being in a PhD program.
7CellBioGuy7yAs a fellow biology PhD student with a somewhat different experience (with you on the work hours, but I'm really glad I'm here), I hope you don't mind me asking what has been so draining about the experience?
7drethelin7yFrom what I've seen people who have been wasting away in academia and described their position much like yours have become WAY happier when transitioning to the private sector.

Just wanted to say good job for realizing the problem was probably with this job, not with you. You may find it helpful, motivationally, to talk to friends/acquaintances and ask them what they like best about their job, so that "a job that doesn't make you miserable" feels more achievable and you feel more hopeful/driven about pursuing it.

I say this b/c a friend of mine was miserable at his job, and I realized how miserable when I told one funny story about my workplace, and he wondered if he could work there, specifically, because I didn't seem... (read more)

Coding + stats skills + some biology = the world is your oyster (pharma, research labs/institutes, postdocing if you aren't sick of academia yet, bio startups if you feel you can get invested in something again, etc). I am sorry you had a toxic experience in graduate school. I know this does not help, but I can tell you these are very common, especially in your field.

9Punoxysm7yAsk your professors and school career services and fellow students what are some good non-academia career options. Most people who get a PhD in your field aren't going into academia, so where are they going? Research Labs and Pharma/other medical companies (which I imagine are your major prospective employers), or some bio-oriented software companies will have wildly varying work environments. Do your best to choose one that seems to have a friendly, lower-pressure environment. Cultivate your life outside of work, and make friends inside. Save some money. There's good odds that the professional world will treat you better and demand less than your PhD program. Then figure out where you want to go from there.
The Octopus, the Dolphin and Us: a Great Filter tale

That's a good point. I guess not. My intuition is that a lot of organisms have evolved simple multicellularity, and so would probably be doing better as unified multicellular organisms, but it's possible, as you say, that they haven't gotten to that point for lack of the niche. I don't know enough about the topic to say.

The Octopus, the Dolphin and Us: a Great Filter tale

Yes. And this is what has happened to most branches of the tree of life. E.g. Archae Bacteria, the various Protists. Only very basic multicellularity occurs in most kingdoms.

The Octopus, the Dolphin and Us: a Great Filter tale

Agree. the road from creation of life to creation of any nervous system at all is an extremely long and fraught one.

Life on our planet has a very specific chemistry. It's possible that almost all possible chemistries limit complexity more than ours - leading to many planets of very simple organisms. Very large number of phyla on earth reach evolutionary dead ends both archae and bacteria are stuck as single cellular organisms, (or very simple aggregrates) - Plants cannot develop movement because of their cell walls, while insects cannot grow bigger becaus... (read more)

5Houshalter7yCould it be that different niches of life don't independently evolve because those niches are already being filled? Can we say with confidence that if all animals died, something like animals wouldn't eventually evolve again? Or any order of life.

This is another good explanation instead of / in addition to the Great Filter.

It could be that there are many local optima to life, that are hard to escape. And that intelligence requires an unlikely local optimum. This functions like an early Great Filter, but in addition, failing this filter (by going to a bad local optimum) might make it impossible to start over.

For example, you could imagine that it were possible to evolve a gray goo like organism which eats everything else, but which is very robust to mutations, so it doesn't evolve further.

Open thread, 23-29 June 2014

I used to get these split second emotional flashbacks all the time, primarily when stressed. They were usually about embarrassing or frustrating moments, and would very frequently cause some kind of verbal twitch - usually these compulsive phrases like "I want to go home" or "I hate this place" or "I hate myself". Very embarassing in the rare instances it occured around other people.

Meditation seems to have brought down their frequency a lot. Or at least, of the many things that have changed, the frequency with which I meditate seems to correlate most closely.

Rationalist Sport

I hate to sound machiavelian here, but i think an important criterion for a good sport missing from this discussion is "gain friends, respect, and a conversational topic with people who don't identify as rationalists".

A lot of us are going to be short on opportunities to achieve these goals. So the most instrumentally rational sport may be the one which happens to be popular in your immediate social environment.

2ChristianKl8yI think the skill of holding a conversation is much more important than having conversational topics. If I wanted to optimize for that goal I would do Improv Comedy as a hobby. A lot of sports give you a new social environment when you practice them. You don't have to optimize for your existing social environment.
Rationalist Sport

Boxing is a great sport on almost all of the above criteria. Unfortunately, it's not an option for those with a preference for keeping their blood and their spinal fluid separate.

2NancyLebovitz8yFair point. Chess-sprinting? Could prasara yoga [https://www.youtube.com/watch?v=YK6CGtViWg8] be made into a sport? Should it be?
Positive Queries - How Fetching

Also a chronic loser of keys. In addition to what's been suggested below - are your keys heavy enough? MIne have, e.g., a bottle opener and a usb key on them, and a very thick ring. The bottle opener in particular makes it difficult for them to slip out of a pocket, and the whole thing is heavy and noisy enough that a) it makes a lot of noise when dropped b) I can easily check for it's presence by patting my pants. Getting into the habit of doing this whenever leaving a location has saved me a lot of hassle.

0VAuroch8yI solved this a slightly different way: I found a very thin wallet (more of a flat coinpurse, really) and put my keys and a couple other cards in it. This makes it heavier (which helps) and sit cleanly in my back pocket; checking that it's there doesn't even need a pat. In theory, this increases the potential loss if I do lose my keys, but increasing the stakes also makes me check more often. (I'd found this previously when I bought a semi-expensive mechanical pencil instead of a box of new ones, and proceeded to keep track of it for longer than it had taken me to go through a box of 12.) It also has other benefits: I keep my money in a separate, garden-variety wallet, but always keep at least $25 in the key-wallet for a bus ticket or short cab ride home, which is a nice hedge to have.
0torekp8yFellow pants-patter here. Also, before bed I get my tomorrow-pants set up with keys, wallet, etc. before throwing the current ones in the laundry pile. More generally, strong habits can compensate for much in the way of weak memory.
2aisarka8yThanks. That's fixed. I also checked all the other links in the post for 404 errors and fixed two others.
Open Thread March 31 - April 7 2014

though I am willing to accept an argument on statistical distributions and number of trials.

I would expect english media to just be better on average, due to the larger, more competitive market. Is this what you mean? (I imagine the foreign language/emotional reaction effect is the dominant thing going on though)

Distribution of knowledge and standardization in science

A modest proposal: Anyone wishing to create a file format will be forced to write out a 10 megabyte example of the format, by hand, without error, before the new format will be accepted.

What are some science mistakes you made in college?

If I had only had this advice at the beginning of my PhD, I would have saved myself a lot of hassle....

Also, the above advice would suggest, for instance, that we should use SAP's ridiculous, bloated crapware to manage human resources etc... Sometimes the multibillioner dollar companies fail.

7aarongertler8yWell, "learn from it" and "use the crapware" can mean different things. I've found useful the rule of thumb that "someone else once had your problem and you should find out what they did, even if they failed to solve it".
What are some science mistakes you made in college?

One key meta mistake you see a LOT in computational biology is people not seeking out the proper expertise they need. I and countless other people have wasted months re inventing existing tools because I had no idea they existed, which is turn was because there were no experienced researchers around me with the relevant expertise to tell me.

5aarongertler8yIndeed! I found this to be an extremely helpful resource w/r/t seeking out "meta-expertise": http://faculty.chicagobooth.edu/jesse.shapiro/research/CodeAndData.pdf [http://faculty.chicagobooth.edu/jesse.shapiro/research/CodeAndData.pdf] Key quote: "Here is a good rule of thumb: If you are trying to solve a problem, and there are multi-billion-dollar firms whose entire business model depends on solving the same problem, and there are whole courses at your university devoted to how to solve that problem, you might want to figure out what the experts do and see if you can't learn something from it."
Load More