Rachel Berkson

Rachel Berkson

Education Manager at Wellcome Connecting Science, UK. Background in cancer genetics then education. Particularly interested in inclusive education.

Location UK

Activity

  • In step 3.13, you will find a text entry box where you can submit the report for your assignment. You don't need to paste it into the comment section. Unfortunately FutureLearn accepts only plain text submissions, but if you include URLs, your reviewer should be able to copy and paste them to open the web viewer.

  • Great answer. We hadn't anticipated that URLs might be too long for the discussion section altogether! If you run into this problem again you can try a link shortener such as tinyurl.com

  • Great! The last Activity at the end of week 3 will show you how to do this on a technical level. Completing week 3 should also give you a clearer idea of what sort of analysis you can do once you have installed BTK on your own computer.

  • Hi Asime. I can see you've applied some filters based on GC content and coverage, but you still have mutiple sequences in your plot. You might want to choose a region of the plot that only has one circle away from the rest of the plot, so that you can easily filter down to only one sequence.

  • Hi Taiwo. You may want to change the view from squares to circles - the squares view is the default when an assembly has a very large number of small contigs. You'll learn more about this is in week 2. For now, go to the Settings menu, and select the circle icon from the Shape menu. See if that gives you a plot that might be easier to understand.

  • Hi there, I hope you're enjoying the course. Please avoid copying comments from other learners. That makes it hard for the Educators to understand what ideas are yours and what support you need.

    Just to let you know, you don't need to comment on every step. If you just click the "Mark as complete" button when you've done the step, that's all you need to...

  • Hi Alexandre, you did well at finding an organism and generating the BTK plot for your sparrow. Just be careful about reporting GC content - it's on a scale from 0 to 1, so when you read 0.4 off the X axis, that means 40% GC, not 0.4%. The percentage of GC in the genome will always be somewhere around 50%, you wouldn't expect to see a genome with 200X as many...

  • Good analysis! There could potentially be two different proteobacteria in the assembly but it's more likely that one very small contig has been assigned incorrectly. In week 2 you'll learn more about how to drill down into more detail and examine the evidence for how many different species are really present.

  • No-hit means that Blast was not able to find a definitive match to a known organism. The colour assigned to no-hit here is quite similar to the light blue representing Ascomycota, so it's hard to see, but these contigs (which happen to be quite small) are present in the plot. Later in the course you'll learn about how to use filters to examine no-hit blobs...

  • This is a great question, @RachelGray . In week 2 you'll hear more about how to deal with assemblies where some of the information is missing.

  • Thanks for this report, Keeley. It seems that some learners didn't fully understand the assignment task, which points to problems with how the course is constructed. I'm sorry that you had a disappointing experience with peer review, but I hope you found it informative to work on your own course design.

  • I'm really glad to hear that you got some useful and encouraging feedback as well as the disheartening response that didn't match the effort you put in. It definitely is useful for us as educators to hear that the peer review task was only partially successful. We'll be reflecting on how to improve the instructions for submitting and marking the assignments...

  • Thanks for reporting on your experience, M G. This peer review task was fairly complex, and it's a useful learning point to realize that not everybody understood how to complete the assignment. Thanks for persevering and giving what feedback you could, even if one of your assignments didn't have a clear structure.

  • @SusanC @KeeleyMcCabe I understand your concerns. Although the course is officially three weeks in duration, the educator team are still around and we do try to catch up with comments that have come in a bit later. The course will remain open for 6 weeks after the official end date, so you will still have plenty of time to review the material and work on your...

  • Thanks for reporting that you were unable to see the video. I'm sorry that you had that experience; the best suggestion I have is that you can read the transcript linked below the video and in the Downloads area. That way you can read what this week's instructors have to say even if you can't hear them.

  • That's great, Bahar. Much clearer articulation of the aims and goals of the course. I look forward to seeing how this develops as you work through this week and next.

  • @SusanC I find H5P really easy to use - they have a lot of pre-built templates that you can just slot your content into, but also flexible as you can tweak the code as much as you need to. Personally, I have only used the site as part of FutureLearn courses ie purely online, not in a face-to-face classroom.

  • Can you say a bit more? What aspect of Public Health Genomics? Can you think about your goals and objectives and why this training is needed?

  • This is a great idea, Mara! Effective design is important in informal training too. A short lab meeting activity introducing the Pseudomonas genome database sounds like it will be really valuable both for you and your colleagues.

  • Your learning outcomes are coming together and give me an idea of the level and content of your course, which is a great start. The one about the Unix command-line could do with more specifics; what sort of data? What sort of analysis? Using the command-line is a fairly complex skillset in itself, so perhaps you could give an idea of the level of competence...

  • This set of LOs gives me a pretty clear idea what will be in your course. I think perhaps the first one would benefit from some refinement: how will you know whether students understand these key concepts? Will they be able to explain them? Use them in calculations? Use them to describe or predict the behaviour of a structure?

  • Interesting to see enthusiasm for hybrid design in the comments here. Hybrid really can be the best of both worlds, but be aware that it can be a lot of work to create training that can work in either format. If you need flexibility to be able to switch formats at short notice, or if you have a mixture of in-person and online learners in the same activity,...

  • A workshop giving an introduction to the field could be a great design project. I'm interested to see what ideas you come up with as you progress through the course.

  • That's a great question, Aneth. I would say giving adults a say in the content and process is not the same as giving them completely free choice with no direction or guidance.

    For example, the curriculum may specify that the students need to learn how to perform a sequence alignment with a particular tool, but you might give them a choice of exactly which...

  • I like Nicole's description that undergraduates are "between adulthood and childhood". There is no hard-and-fast rule about the exact boundary of who counts as an adult learner - it depends on the context, the culture, the structure and expectations of the course etc. Personally I have facilitated successful learning activities by applying andragogy...

  • What an amazing example of using reflection and evaluation to improve your teaching, and seeing a measurable impact.

  • @HeatherGibling That's fine, Heather. The course will remain open for a further 6 weeks after this weekend. If you submit your assignment next week or later, you will be 'paired' with another learner who is also taking things a bit more slowly, so that hopefully you will get feedback and get an opportunity to review another learner's assignment.

  • Please can you avoid copying and pasting comments from other learners on the course? You don't have to reply to every step - just clicking the 'Mark as complete' button will register that you have done the step so you can get the certificate at the end of the course. If you copy from others it's hard for fellow learners and Educators to know what is really...

  • It's impressive that you were able to change the course on the fly to cover more basic research skills. This is a really good illustration of why it's important to find out as much as possible about your students' prior knowledge, and also to be flexible and responsive as the course progesses.

  • That's a really good observation. We've had similar trouble with live online sessions, if trainees don't have reliable internet access there can be real problems. You came up with a good solution by following up afterwards to check progress and understanding even if trainees couldn't attend the contact sessions. But that does create a lot of extra work for the...

  • It's certainly hard to argue that we need experts in detection and surveillance of viral infections! It will be interesting to see as the week goes on how you will approach training people in these skills. You're looking at producing experts, and you've outlined that your learners will need to know a lot of different areas; doing PCR to amplify viral genomes...

  • Great start. I particularly like how you've divided up your theoretical knowledge from your practical skills. Having those categories clear in your mind should help with designing appropriate learning activities.

  • Your description sounds good to me. At this stage we're only trying to decide the high-level objectives for the course, it's fine if your specific learning outcomes need a bit more refinement before you're ready to submit your final project.

  • Creating an MSc module which can also be a stand-alone course can be a real challenge, and it's likely to prompt some really strong design decisions. I'm looking forward to hearing more about this as the next two weeks progress.

  • Interesting concept, designing training for one person. Many of us have to train new colleagues but we may not put thought into the design as the training happens fairly informally. Starting from good design practice could be really beneficial here!

  • It will be really useful to be thinking about improvements for a course you have already run for real. What do you think would make the biggest difference to your analysis module?

  • That's great, Heather. We recently developed a similar course as a FutureLearn MOOC and there was huge demand for those topics. The course isn't currently open but you can have a look at the landing page with overview and learning outcomes: https://www.futurelearn.com/courses/linux-for-bioinformatics/1

  • This course uses the basic format of a MOOC (massive open online course), and the learning approach is referred to as 'conversational learning' with the emphasis on the discussion section. Another term I might apply would be 'semi-synchronous' - although you are not all online simultaneously, you are working through the material at roughly the same pace,...

  • To clear up some potential confusion: when we refer to 'evaulation' in this course we are talking about evaluation of the course or learning activity itself. We use the term 'assessment' to refer to measuring the performance of students. Of course, knowing how the students are doing and whether they achieve the Learning Outcomes might be one element of your...

  • The Bloom pyramid is by no means the only way of classifying different learning activities and outcomes, it's just very commonly used in education. The important thing is to make sure your learning plan is aligned: the learning activities and assessment should be relevant to the level of the intended outcomes.

    As you point out, if you want learners to be...

  • That is a great point about the difficulty of adaptation to the learners' needs in an asynchronous course. The approach we are using here is for educators to monitor the course, and if we see that several learners are struggling with a particular topic or activity, we can "pin" a comment with further explanation or additional resources at the top of the...

  • This is not necessarily true. A short course can be very suitable for learning to analyse or evaluate. Learners might already have a good grounding in the subject area and are looking to build their skills in a specific technique. They might for example look at some previous experimental results and apply statistical methods to that data to argue for or...

  • This seems like a good approach, Faisal. In this short introductory course there isn't enough time to develop a whole MSc, but you should be able to apply your learning to the design of an individual module.

    The educator team mainly specialize in professional training, and we have drawn most of our examples from that domain. We do have experience in Higher...

  • When we refer to 'evaulation' in this course we are talking about evaluation of the course itself. We use the term 'assessment' to refer to measuring the performance of students. Of course, knowing how the students are doing and whether they achieve the Learning Outcomes might be one element of your evaluation, so you could use assessment data as one of your...

  • This is a great framing, I love the idea of teaching students, that is people, rather than only teaching a subject. We'll be discussing a lot more about bringing in students' life knowledge as we go through the course.

  • It's not an uncommon situation that the people who become educators were the ones who were most highly motivated by their learning as students, so may not fully understand how to teach groups with more mixed levels of interest. It is good to reflect on how to design activities with broad interest and appeal, and also how to harness that inherent passion when...

  • You're absolutely right that training to bridge disciplines is a key challenge in bioinformatics especially, and one we will be discussing throughout the course. I like your range of examples here: biologists may be put off by too computer science, or may want more detail than can be covered in a short course.

  • I really appreciated hearing from clinicians and scientists about how new technologies are impacting practice now and what might change in the future.

  • Rachel Berkson made a comment

    I think there's a lot of potential in gene therapy such as described in the article, where it is used to enhance autologous stem cell transplantation. I'm not convinced it will ever be possible to cure genetic diseases by direct gene editing of differentiated cells though. The recent preliminary results in Duchenne Muscular Dystrophy are really encouraging and...

  • Great examples - but these are all single gene tests, not genomic!

  • This is a difficult one. Generally targeted therapies are more expensive than traditional chemotherapy, and biologics are fantastically expensive. Some money will be saved by not treating people with ineffective drugs, and dealing with fewer adverse reactions. My main concern is drug development though; it is very difficult for companies to get ROI from...

  • I only half believe in personalized medicine. I love the idea of looking at someone's genetic profile and using that to inform what drug should be prescribed. But it seems like one of those technologies that's always just around the corner. I think there's a lot of mileage in partial steps, like, ok, we can look at a small panel of genes to decide whether...

  • In theory I'm happy to just hand over my genome and associated family history to my GP - I trust her personally, and I'm lucky to belong to a really good practice. But it really seems urgent to improve the level of protection for medical data, before genomic information is routinely available. There have been too many cases of medical data shared with...

  • We're probably quite close to the point where at least some genetic testing is cheap enough to do in a primary care setting. If we get there, it will be like any other diagnostic test: ideally used to support a GP's clinical judgement. In reality there may be some tendency to over-rely on a test that gives a quantitative or yes/no answer, at the expense of...

  • My family is an extremely cardiovascular family, relatives on both sides basically always die of some kind of heart problem. Very little cancer, very little diabetes. Most of what is recommended for heart health is generally a good idea anyway, such as eating healthily and doing plenty of exercise, so I haven't taken any special precautions. I have siblings...

  • The advantage of a cardiac autopsy would be that the relatives might find comfort in knowing the underlying cause of sudden death, rather than it being a complete mystery. If the cause of death was genetic then relatives could be tested. The disadvantage is that it requires a very skilled pathologist and most importantly that PM diagnosis is too late to save...

  • I would say in the short term use of genomics methods to track outbreaks of infectious disease and prescribe the right antibiotics. That is because the technology to do this is already mature and is available cheaply enough for use in low-resource settings where the burden of infectious disease is particularly acute. We are also in the middle of an ID pandemic...

  • I had never really been clear on the advantages of CGH over karyotyping, and this week has really cleared that up for me. I feel I have a better understanding in general of which tests are used in which clinical circumstances and what information is available from each.

  • I'm not convinced by replacing 'mutation' with 'mistake'. I would generally say that 'mutation' is a fairly commonly known word. Perhaps the first time it's used, the doctor might say, 'a mutation, that's like a type of change or mistake in your gene', but after that use the term 'mutation'. For me, a sentence like "And the family history in you, Mrs....

  • There is a shift in NHS culture from writing referral letters from specialist to GP, towards addressing referral letters directly to the patient. In this case I think the primary audience should probably be general clinicians. The report contains highly specialist information and it is the job of the clinician to be able to interpret it in a way that is...

  • I think ethnic divergence among SNPs often indicates a founder population or bottleneck effect, where all people from a particular area have a recent common ancestor in common. The rate of mutation of a particular nucleotide position is quite low, so most people in a population of a particular ethnic origin would share the same SNP as their ancestors. An...

  • I think the fact that genome sequencing generates so much data that computer assistance is needed to analyse it could introduce a new set of problems. What if the computer's algorithms are inconsistent or based on wrong assumptions in the model? It would probably take a long time to find out. A clinician can use their judgement to interpret a simple test, but...

  • 'Copperfastened' is a new word for me! Thanks for that. I am not sure the GDPR is strong enough to rely on for genomic data, information commissioners don't have sufficient power to deal with medically significant breaches I would say.

  • My initial thought is that long-term, secure storage is both a technical and an organizational problem. Supposing the NHS stores my genome on a huge computer today - in 10 years' time, will the file still even be readable? But more seriously, will the NHS still be a publicly owned and widely trusted organization? There have already been controversies over EHRs...

  • Well, I'm an educator so a big part of the impact of new technologies is that I constantly have to update my training material so that we are talking about the latest best practice, not some old methods from years ago! Another impact is that the volume of data generated by genomics is too vast for any human to interpret, so everybody has to have some knowledge...

  • I have an ovarian cyst, it was an incidental finding from an investigation for something else. Most likely it's completely harmless, but there's a small chance it could burst. The gynaecologist who discussed it with me did a good job of explaining that I could choose to have surgery or could choose to ignore it, and gave me enough information to decide. Other...

  • Of the remainder, a great deal of DNA is regulatory elements which help to decide when the protein-coding genes get expressed. Some regulate individual genes, and some control larger chromosome regions, controlling the architecture of the DNA. Some of the DNA codes for functional RNAs - they are never translated into proteins but have important effects in the...

  • I think we have all the tools, between NGS and CGH. But just having the tools doesn't mean we understand the genetic basis of all diseases. Many genes, even protein-coding genes, have completely unknown function and even when we do know something about what a gene does, we don't fully understand why a change in that gene causes a particular disease. Also,...

  • I would consider 20% risk of a heart defect to be high risk. Autism and learning difficulties are hugely variable and it's hard to judge risk based on just a number, but 40% still sounds quite high. I would definitely want to know more about the experiences of other patients with similar conditions to the one my child had.

    Explaining risks in a way that...

  • One advantage of array CGH is that it might detect a deletion or insertion even when the gene underlying a condition isn't known. A deletion of 100kB is likely to be significant, whereas a point mutation detected by gene sequencing might be an irrelevant passenger mutation. However, if a region were deleted that wasn't known to contain relevant genes, it might...

  • I think had Venter succeeded in patenting genes, it wouldn't have made that much difference in the long term. His patents would have expired by now in any case! Most likely those patents would have been legally challenged and overturned, as Stephen says there's no clear legal basis for patenting something that is not an original invention. I also agree with...

  • I work at the Sanger campus which contributed a major part of the work to the public, collaborative Human Genome project, so I'm very biased towards that method of doing science. My colleagues still work like this today, for example spearheading a collaborative effort to sequence tens of thousands of SARS-CoV2 genomes with the aim to understand and control the...

  • The thing I found most difficult was trying to find any follow-up on what has happened with mitochondrial donation babies in the UK since they first started the programme in 2018. I've drawn a blank on that and I'm really curious whether it worked out. Otherwise I'm pretty familiar with modes of inheritance, indeed it's a class I taught in medical school for...

  • I think for me I would only be tested if there was something I could do about the findings. I wouldn't want to go through my life knowing that I had a condition like Huntington Disease, which would certainly kill me but I couldn't do anything about it. (I don't have children or plan to, and none of my siblings have shown any interest in having children, so the...

  • Hi Navid. Normally with these courses you can only get a certificate if you pay to upgrade. That's how FutureLearn make their money. If you look at the top of the page you should see a link saying 'Get extra benefits' and that will take you to the shop to buy the upgrade. In theory it doesn't matter what country you're in, as long as you are able to make an...

  • I really think the use of donor mitochondria to avoid severe disease is ethical and desirable. I understand general concerns about reproductive cloning but I agree with the position of the UK HFEA that this should be an exception. I don't think a child with a tiny amount of mitochondrial DNA from a donor meaningfully has three parents (and honestly it wouldn't...

  • I notice the Taussig article is from 2014 - there have been significant advances in gene therapy since then, so I wonder if his two boys would be eligible for experimental treatment. They will still be pre-adolescent so within the window when treatment is likely to be possible.

  • A colleague linked to this short documentary of people talking about their experiences of genetic diagnosis. I was particularly struck by the person with the BRCA1 cancer-prone mutation who wishes she had known earlier so she could have had prophylactic surgery and not been so focused on marriage and having children. (Relating back to the discussion about...

  • It's completely crucial that different specialists collaborate and communicate with each other to support patients with complex conditions and especially multi-morbidity. Most genetic conditions are individually rare and generalists are unlikely to have enough knowledge to diagnose and treat. It seems here that Heleni has benefitted from continuity of care:...

  • As we saw in the earlier article, the proportion of cancers which are hereditary is small. And for most cancer-prone syndromes prophylactic surgery like this isn't an option. For example if someone has Li-Fraumeni syndrome, born without the tumour suppressor p53 so essentially a congenital mutator phenotype, well, there's no surgery that's going to fix that....

  • So one thing I'm confused about: autosomal conditions should affect men and women in equal proportions. But a mutation in BRCA1 is presumably far more likely to affect women. In Jolie's case it was three female relatives who died of breast cancer and no men. I know men can sometimes get breast cancer, but if they have the BRCA1 hereditary syndrome, and have...

  • Personally I found the Wu et al Nature paper a lot more convincing than the Tomasetti & Vogelstein Science paper. The criticisms of the mathematical assumptions used by T&V seem apt to me. Further, Vogelstein has spent much of his career assuming that all cancers are basically similar to colorectal cancer, which is not really a valid assumption IMO.

    That...

  • I love this (well-referenced) blog posts about gynandromorphs, which are mosaic in sex chromosomes. http://biologicalexceptions.blogspot.com/2015/05/half-male-half-female-completely-weird.html
    I'm particularly enjoying the lobsters http://4.bp.blogspot.com/-_UK4X0clvQ0/VRsE_YDAhhI/AAAAAAAADvs/Nr-eFQ0zfRk/s1600/3-splitlobster.jpg but not everybody finds...

  • I am glad the Welcome to Holland framing is helpful for some families, but I know a lot of disabled people dislike how much it's focused on parents' expectations rather than their own life experiences. It's good to see that Alice in this video gets to speak for herself a little bit.

  • I was surprised when I learned that the chromosomes are actually numbered in size order! Well, roughly, it was done based on just light microscopy rather than genomics.

  • The first week was introductory for me; it's all areas related to my own research. I was interested to see the creative use of multimedia even during lockdown, lots of animations instead of the usual videos. Including some of my team's material from the Your Genome website, I note.

  • Agree with everybody who's said that epithelial progenitor cells are the fastest to divide. Many cells are terminally differentiated and have stopped dividing altogether. A possible contender for the slowest dividing cells is oocytes: they get part way through meiosis in the embryo and remain in suspension for as long as multiple decades before finally...

  • I imagine the cell like a factory. The genome is the set of instructions and SOPs for working the different machines on the production line. The transcription factors are like the foreman who decides which machines should be working today. Epi regulation is more like the health and safety inspector - they may cordon off part of the factory where the roof is...

  • For most of evolutionary history the environment changed relatively slowly compared to a generational scale. If a pregnancy started during famine then there's a high chance the offspring would spend much of its life in food scarcity so epigenetic adaptations to calorie deficit would be advantageous. Humans are unusually long lived and human technology can...

  • Rachel Berkson made a comment

    Check out this absurd little protozoa, a single-celled organism with over 16 *thousand* chromosomes: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558436/ I think 'more complex' isn't necessarily well defined, but I was tangentially involved in some research which suggests that complexity scales with the number of transcription factors (regulators of which...

  • @stephenHalston I agree, there's unlikely to be a better example than this. There is no limit to the amount of information that can be encoded using a binary system, with computers being the classic example. DNA is very physically compact - it's hard to think of another system which encodes so much information in such a tiny volume. But expressing complex...

  • Hi all. I'm a molecular biologist by training, and have worked in medical education for much of my career. I work as education manager at the Wellcome Genome Campus Advanced Courses programme near Cambridge in the UK. My team are currently working on a FutureLearn course on genomics in primary care and I wanted to check out this course on a related topic.

  • 3. Crowdsourced doc on Teaching Online with Care (via Martin Weller) https://docs.google.com/document/d/1HhxP-E0cQLkbTgkMIAxmMK_LH5ttgV3OTSBf5IK983M/edit#heading=h.2ms4wwwjw8k0 This is less useful than #1 and #2 as it's not very curated, and I would need to take time to go through it in detail to find specific resources I need, but it's valuable to me because...

  • Evaluate: the most useful links I found by looking through these directories were:

    1. The Quality Matters Emergency Remote Instruction Checklist https://docs.google.com/document/d/e/2PACX-1vRzSgvQZDAbu9iG3Cxnq3D2hlxiUZrzwVRj94MGPVDvY9exqxiSgOkuhKxkexPSxb12cb3QNqDTWSIc/pub (from the DCU directory) Having a well-evidenced checklist is useful for both design...

  • Search: the context I'm looking for is advanced training, mainly for adults, but outside HE. So I wasn't able to pull out material from this list using a simple keyword search, I had to quickly skim the descriptions and work out what I wanted.

    Filter: my top three collections were:
    * The article by Martin Weller...

  • @RebeccaFerguson Thanks so much. That's a really helpful connection. We have been working with the team at Bath University who have also done some evaluation of healthcare-related MOOCs, but everything has got a bit disrupted with the pandemic, and it's a good time for us to be building a network of experts in online learning.

  • For my main online training, we are now part way through week 3 of a really successful FutureLearn short course. My priority as we wrap up the live part of the course is to find evidence of impact. Many of the students are healthcare professionals or involved in research that supports healthcare, so we want to know whether our course has made a difference to...

  • I had an in-person Sunday school class (8-11 year olds). We cancelled the last couple of classes before the break, and now we are resuming with online-only when the new term starts. I think my first priority with that group is getting them used to interacting in a Zoom environment. They are often distractable even in person, and social dynamics can be...

  • I'm going to send out reminder emails to my educators' team (who are new to FutureLearn) with some suggestions for how to promote good social learning discussions.

  • I teach an online class for a small group of 10-year-olds; it's a replacement for Sunday School. I use games to encourage the children to interact with each other even though they are in different locations. For example, this week they will take it in turns to draw something related to the topic and hold it up to the camera, and then the other children will...