6,606 reputation
13162
bio website blahah.net
location Cambridge, UK
age 28
visits member for 2 years, 5 months
seen Jul 5 at 12:24

PhD student in Plant Sciences at Cambridge working on dissecting the molecular basis of C4 photosynthesis. Formerly plant biologist, data analyst, bioinformatician and programmer at the Millennium Seed Bank.

My expertise is in plant biology, genomics, transcriptomics and computational biology.

I write software in Objective-C, C++, Ruby, Python, Javascript and R.

Solvers.io is my attempt to help highly skilled developers use their skills to benefit the world's poorest, or to help solve crucial scientific problems.


Jan
4
comment Is light required for seed germination?
@KonradRudolph in many species, germination can happen underground but not so far that light doesn't penetrate.
Jan
4
comment Is light required for seed germination?
The short answer is that many species do require light for germination (either to initiate germination or to break dormancy). Some require light of a specific wavelength, and some don't require light. Still others actually require absolute darkness, or the absence of specific wavelengths.
Dec
31
comment Seed Dormancy and Seed Transportation
I'd just like to say how happy it makes me to see primary and secondary dormancy being discussed on bio.SE: very happy indeed :). Also: this is exactly the answer I would have given.
Dec
30
comment Why is dimethyltryptamine (DMT) being released during death?
As with many such questions, it may be impossible for us to infer why this trait evolved.
Dec
30
comment Why is dimethyltryptamine (DMT) being released during death?
This doesn't answer the question. The question asks why DMT being released at death would be selected for evolutionarily.
Dec
30
comment Why is dimethyltryptamine (DMT) being released during death?
I disagree with all of this except the part about evolution not being a conscious designer. You are arguing that genetic drift accounts for a large proportion of evolution. This is the opposite of the current understanding informed by genomics and transcriptomics. For example: onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2007.00308.x. It is highly likely that there is a reason (i.e. a proximate cause) for DMT being released at death, but it may not be direct, and it may be impossible for us to infer it with current information. The same is true for having 5 fingers and 2 arms.
Nov
8
comment Measuring algae growth or death
I've asked some of my colleagues who work on algae to chip in... hopefully one of them will turn up :)
Nov
4
comment How long can I store extracted RNA?
We're also in an old dusty building, and RNase is a problem for us too. Thanks for the tip - I'll check whether it works for RNAseq purposes.
Oct
29
comment How long can I store extracted RNA?
This is interesting - how did you measure the degradation? I imagine degradation that might have a significant effect on, for example, RNASeq, would not show on a gel.
Oct
29
comment How long can I store extracted RNA?
Do you need to do anything special to remove the citrate when it comes time to use the RNA, for example to make cDNA?
May
23
comment What is this marmot-like animal (Tigray, Ethiopia)?
It's definitely not a rock hyrax, it looks a lot like a ground squirrel.
Oct
19
comment Why does high-voltage mostly shock a person, and even small current kill?
It depends entirely where the current passes through. If the circuit is completed through your hand, you are unlikely to die no matter what the current. But it it completes across your chest, you run a much higher risk of fibrillation and heart attack.
Oct
13
comment What does “delineate” mean in this context?
Didn't think of that!
Oct
13
comment What does “cellular” mean in this context?
Diatoms are generally porous, so perhaps that's why they thought it might mean that. But I've never known 'cellular' to mean porous.
Sep
20
comment Transcript(omics) terminology: cDNAs, ESTs, RNA-seq, etc
I think RNA-Seq assembly prior to alignment is common in non-model species, where you need to first describe the features you align the reads to.
Sep
20
comment Does culling badgers restrict the spread of bovine tuberculosis?
Much better :) +1 For an even better answer you could summarise the main points?
Sep
20
comment Does culling badgers restrict the spread of bovine tuberculosis?
This doesn't answer the question...
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
Probably both. Berkeley Madonna is specifically for modelling, but it's horrible, so it's not that widely used.
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
It's not the chance of both eggs being excluded that Dawkins talks about, he talks about the chance of having an egg excluded. It's still true that it would be worth cheating for the first few birds. The wider point about the trait not being an ESS might be true, but his specific explanation is not. In your specific example, if there are 105 eggs and 5 are excluded, each egg has a ~5% (more precisely, 4.76%), not ~1%, chance of being excluded. In any case, your question was interesting so I'm writing a model of the Guillemot situation. I'll report back when done :)
Sep
10
comment Difference between genetic engineering and synthetic biology
PCR is not synthetic; although it involves biological synthesis, it has to start from a template. Synthesis as in synthetic biology involves artificial gene synthesis, i.e. starting just with a sequence on a computer and ending with biological sequence.