I dont know anything about AFM however one observation I have made seems to be clear – that is, in the AFM of surfactant protein D the peaks along the arms of the dodecamers cannot be the result of bouncing or secondary blips in the motion of the “tip”…. since they would all then need to be arranged in the direction of the dragging of the tip and they do not appear to be aligned in any particular direction.
Monthly Archives: December 2019
Just doesn’t matter: freehand, straight line, rectangle
Not much changes the height plot in AFM images if the peaks are readily discernible with the naked eye (brightness peaks counted by hand awas 11) then changing the properties of the bounding box in LUT plot (plotted peaks = 11) analyses just really doesn’t make much of a difference…. at least in this example it matters precious little. These plots were aligned from the tip of the first peak to the tip of the second peak. Plot y axis was not change and exported automatically from Image2-Fiji. Examples of freehand wavy and rectangle below the plots. So after a year or more of trying to figure out the basics methods with which i am comfortable in terms of morphometry are the following.
1) optimize the image to 300ppi
2) measure curve SP-D arms using a vector line which is measured at cusp points (nodes).
3) trim excess (eraser or crop) background away from the hexamer (CRD to Nterminus to Nterminus to CRD on the other end of the hexamer.
4) apply a straightening technique (1nm slices which are centered horizontally)
5) export image as compatible file for ImageJ23Figi (or ImageJ)
6) drag rectangle from edge to edge and at a width that encompasses the most favorable area)
7) analyze>plot profile> then save to excel
8) plot import as metafile to CorelDRAW
9) evaluate imported plot over original image
10) in view>simple wireframe, align plots according to Y axis tics
11) ungroup plots and delete nodes which are below the background grayscale.
12) find center peak (Nterminus joining of the two trimers) and bisect the plot.
13) align each trimer to half the nm of the desired size you chose for your molecule.
14) establish a significant number of tics on the Y axis (5% ??)
15) establish a significant number of tics on the X axis (might choose nm)
16) compare number of peaks observed by “eye” compare with number of peaks meeting significance on Y axis and x axis
17) create a spreadsheet with peak number and peak nm2
18) compare each column of peaks from various plots and various molecules to see whether peaks are significantly larger or smaller than each other.
Ho Ho Ho, so true
Someone in science must have made up this cartoon, send to all faculty by the interim director in the department.
Discrepancy in size – SP-D
I have tried quite hard to figure out why there is a discrepancy (about 122% larger) in the size of the surfactant protein D dodecamers (well all species of SP-D molecules) in the cover image (which is stated by JMB cover description to be 1micron as the bar marker – total relative width of the micrograph) but which when calculated on individual selected out dodecamers is off by considerable amounts…. much larger. I redid this at least three times thinking i was making an error but i am pretty sure that the cover image micron marker (in the text) is not correct. This makes it a little harder to explain when I return all dodecamers to a standard size (to be determined yet, but somewhere around 145 – 150nm from the tip of the CRD on one arm to the tip of the CRD on the other side. If anyone out there is listening or has an explanation… please advise. Image below (top dodecamer) shows a dodecamer from their figure 1 measured with the bar marker for that image, and the bottom dodecamer is excised from their cover image and sized with the magnification given in the cover text.
A short history of the “dooms day” mentality
Music albums, novels, TV shows, films, computer games, real life ancient rituals, astrology, pagan worship, calendars (Mayan), religions, apocalypse … UnameIT.
The word apocalypse is defined: Old English, via Old French and ecclesiastical Latin from Greek apokalupsis, from apokaluptein ‘uncover, reveal’, from apo- ‘un-’ + kaluptein ‘to cover. so this gives us a clue as to one nature of doomsday, that is
1) to obtain hidden knowledge, maybe to gain an edge for survival.
A paragraph from Scientific American article by Daisy Yuhas (in 2012) is here: “University of Minnesota neuroscientist Shmuel Lissek, who studies the fear system, believes that at its heart, the concept of doomsday evokes an innate and ancient bias in most mammals. “The initial response to any hint of alarm is fear. This is the architecture with which we’re built,” Lissek says. Over evolutionary history, organisms with a better-safe-than-sorry approach survive. This mechanism has had consequences for both the body and brain, where the fast-acting amygdala can activate a fearful stress response before “higher” cortical areas have a chance to assess the situation and respond more rationally.”
2) to be able to take comfort in KNOWING when the end is coming… by prophesy or guessing.
This might allay fears and allow one to just “wait languidly” for the end to come.
This blog actually has some interesting ideas. And a combination of conspiracy and doomsday believers make up a vocal and determined religious group.
Here is another interesting take on doomsdayers – or survivalists… the preparedness for the end.
Earliest recorded apocalypse predictions are associated with the three Abrahamic religions: flood, rapture, tribulation, armageddon last judgement, second coming of Christ, natural disasters, astronomical events.
Quote from wikipedia: “According to psychologists, possible explanations for why people believe in modern apocalyptic predictions include mentally reducing the actual danger in the world to a single and definable source, an innate human fascination with fear, personality traits of paranoia and powerlessness and a modern romanticism involved with end-times due to its portrayal in contemporary fiction.”
Chronology table from wikipedia: here.
What is interesting is that the number of endtime events recorded has increased dramatically with each passing century. This might still represent a small number of people calling such dates out, because the total number of persons has increased as well. But at least in this century we are looking at catastrophic cosmic events, ha ha.
Advice: – my style
It is better to do something imperfectly
than do nothing flawlessly.
author unknown…
The tone of voice
author unknown
Its not so much what you say
as the manner in which you say it
It’s not so much the language you use
as the tone in which you convey it.
Come here I sharply said, and the child cowered and wept.
Come here i said he looked and smiled and strait to my lap he crept.
Words may be mild and fair
but the tone may pierce like a dart
words may be soft as the summer air
but the tone may break my heart.
For words come from the mind
grow by study and art
but tone leaps from the inner self
revealing the state of the heart.
Whether you know it or not
whether you mean or care,
gentleness kindness love and hate
envy anger are there.
Then, would you quarrels avoid
and peace and love rejoice
keep anger not only out of your words
Keep them out of your voice.
Cutest infomercial song ever — Monty Python galaxy song
Kudos to the writers of these lyrics and melody (you can probably find the melody online but here is an updated more tame and hopefully accurate scientific version) and cute animation too.
Whenever life gets you down Mrs. Brown
and things seem hard our tough
and people are stupid obnoxious or daft
and you feel like youve had quite enough —
Just remember that you are standing
on a planet thats evolving
revolving at 1,000 miles an hour
Its orbiting at 19 miles a second
as its reckoned
a sun which is the source of all our power.
The sun and you and me
and all the stars that we can see
are moving at 12 million miles a day
In the outer spiral arm at 40,000 miles a hour
of the galaxy we call the milky way.
Our galaxy itself contains a 500 billion stars
its a 100 thousand light years side to side
it bulges in the middle 6 thousand light years thick
but out by us its just 1,000 light years wide.
We are 30,00 light years from galactic central point
we go round once every 200 million years
Our galaxy is only one of millions and billions
its an amazing and expanding universe.
The universe itself keeps on expanding and expanding
In all dimensions it can whiz
as fast as it can go, the speed of light you know
12 million miles a second and thats
the fastest speed there is.
So remember when you are feeling very small and insecure
how amazingly unlikely is your birth.
And pray that there is intelligent life
somewhere out in space
cause its bugger all down here on earth.
Order – Chaos – Quilts – Microscopy
Thoughts on the evolution of a scientific and artistic style.
Verge of a Dream: I want love more than wanting tomorrow
I think you told me
you are like
the solar system
cold on the outside,
a blazing interior.
You don’t say there is
no love for the restless
and unsettled.
You can give up
and within the cold
cup of tea, that’s left,
carry every twirl
from that
defeat with
never a sigh of
debt.
And I may break
a glass but instead
of being mad,
you bend
to drink from a
shallow creek,
more exotic than ever.
It is the surprise each
day
that makes me say
I want love
more than
wanting tomorrow.
RB 12 10 2019
Verge of a dream